Summary:

If water isn't available and someone in a desert uses stones for cleaning after relieving himself, it makes sense.

However, the issue with Islam is different. It took Allah 22 years to come to this Logical Ruling that: "Cleanliness should be done with water after defecation, but if water is not available, then one is allowed to use stones."

After the advent of Islam:

The FIRST guidance that Allah revealed, was to use 3 stones to clean after relieving (even if water is available).
The use of 3 stones continued for the next 22 years. Only during the last year of Muhammad's life (i.e. a couple of months before Muhammad's death), Allah revealed the SECOND guidance of washing with water.
During those 22 years, many other RULINGS were revealed regarding relieving oneself (like don't face Qibla while relieving, or not to use the right hand, or not to use the dung or bone etc.). Yet, Allah did not reveal the ruling of using of water.
Allah (i.e. Muhammad himself) learnt this method of using water from HUMANS. During his last year, Muhammad came to know that some of his companions used water after defecation. And those companions further told Muhammad that they used it while some of their neighbouring Jews used to use water after relieving.

Our common sense is enough to guide us that this process was not based on WISDOM. It was an ERROR, where Allah had to take 22 years to give the correct and sensible instructions.

One wonders:

If the revelation had truly come from a 'All-Wise' (and All-Knowing) Allah, it would have given correct and sensible instructions from the very BEGINNING, that cleanliness should be done with water, but if water is not available, then one is allowed to use stones.
Due to the seemingly illogical and contrary-to-wisdom manner in which the revelation was delivered, for 22 years, the Prophet and all Muslims continued using the unhygienic and dirty method of stones, even when water was available.

This suggests that there is no divine being (Allah) guiding these revelations, and that Muhammad was crafting the religion on his own. Since Muhammad was only human, it explains the presence of such human errors within the revelations.

Please also note that today, Islamists blame Western people to be dirty for using toilet paper after relieving. However, it is not only in Islam, but in India and the whole of East Asia, people have been using water to clean themselves after relieving for thousands of years. It is not a religious issue, but a cultural issue.

(1) Hadiths that prove that Allah initially revealed the unhygienic ruling of STONES (despite availability of water)

The following Hadiths show, when the rulings about relieving oneself were revealed, then Allah first made the unhygienic ruling of using 3 stones.

Sahih Muslim 262b, Jami` at-Tirmidhi 16, and Sunan an-Nasa'i 49:

Salman (who was a companion of Muhammad) said that (one among) the polytheists remarked: I see that your friend even teaches you about the excrement. He replied; Yes, he has in fact forbidden us that anyone amongst us should cleanse himself with his right hand, or face the Qibla. He has forbidden the use of dung or bone for it, and he has also instructed us not to use less than three pebbles (for this purpose).

This Hadith proves that these Multiple Rulings about defecation had already been revealed in Mecca, when a polytheist gave these remarks about them. So, the questions are:

Why didn't Allah reveal the use of water along with those other rulings?
Why did Allah make Muhammad and Muslims using the unhygienic way of 3 stones for the entire 13-years-long Meccan period?

And this unhygienic practice of using 3 stones continued in Medina too:

Sunan an-Nasa'i 44:

It was narrated from 'Aishah that the Messenger of Allah (ﷺ) said: "When any one of you goes to the Gha'it (toilet to defecate), let him take with him three stones and clean himself with them, for that will suffice him."

Sahih Bukhari, 156:

Narrated `Abdullah: The Prophet (ﷺ) went out to answer the call of nature and asked me to bring three stones. I found two stones and searched for the third but could not find it. So took a dried piece of dung and brought it to him. He took the two stones and threw away the dung and said, "This is a filthy thing."

(2) Muhammad learnt the method of using water from humans (Jews)

The following verses were revealed about the companions of Muhammad, who used to pray in the Mosque of Quba. Those companions were praised for their purification.

Quran 9:107-108:

And [there are] those [hypocrites] who took for themselves a mosque (i.e. the mosque of Masjid al-Dirar مسجد الضرار) for causing harm and disbelief and division among the believers and as a station for whoever had warred against Allah and His Messenger before ... (While) another mosque (i.e. Masjid Quba مَسْجِد قُبَاء) founded on righteousness from the first day is more worthy for you to stand in. Within it are men who love to purify themselves; and Allah loves those who purify themselves.

Ibn Kathir recorded the following traditions under the commentary of this verse, which tell that Muhammad learnt the use of water from his companions, who ultimately learnt it from their neighbouring Jews (link):

وقال أبو داود حدثنا محمد بن العلاء، حدثنا معاوية بن هشام عن يونس بن الحارث عن إبراهيم بن أبي ميمونة عن أبي صالح عن أبي هريرة رضي الله عنه عن النبي صلى الله عليه وسلم قال " نزلت هذه الآية في أهل قباء { فِيهِ رِجَالٌ يُحِبُّونَ أَن يَتَطَهَّرُواْ } - قال - كانوا يستنجون بالماء، فنزلت فيهم هذه الآية " ورواه الترمذي وابن ماجه من حديث يونس بن الحارث، وهو ضعيف، وقال الترمذي غريب من هذا الوجه، وقال الطبراني حدثنا الحسن بن علي المعمري، حدثنا محمد بن حميد الرازي، حدثنا سلمة بن الفضل عن محمد بن إسحاق عن الأعمش عن مجاهد عن ابن عباس قال لما نزلت هذه الآية { فِيهِ رِجَالٌ يُحِبُّونَ أَن يَتَطَهَّرُواْ } بعث رسول الله صلى الله عليه وسلم إلى عويم بن ساعدة، فقال " ما هذا الطهور الذي أثنى الله عليكم؟ " فقال يا رسول الله ما خرج منا رجل ولا امرأة من الغائط، إلا وغسل فرجه، أو قال مقعدته، فقال النبي صلى الله عليه وسلم " هو هذا " وقال الإمام أحمد حدثنا حسين بن محمد، حدثنا أبو أويس، حدثنا شرحبيل عن عويم بن ساعدة الأنصاري أنه حدثه أن النبي صلى الله عليه وسلم أتاهم في مسجد قباء، فقال " إن الله تعالى قد أحسن عليكم الثناء في الطهور في قصة مسجدكم، فما هذا الطهور الذي تطهرون به؟ " فقالوا والله يا رسول الله ما نعلم شيئاً، إلا أنه كان لنا جيران من اليهود، فكانوا يغسلون أدبارهم من الغائط، فغسلنا كما غسلوا، ورواه ابن خزيمة في صحيحه، وقال هشيم عن عبد الحميد المدني عن إبراهيم بن إسماعيل الأنصاري أن رسول الله صلى الله عليه وسلم قال لعويم بن ساعدة " ما هذا الذي أثنى الله عليكم { فِيهِ رِجَالٌ يُحِبُّونَ أَن يَتَطَهَّرُواْ } ، الآية " قالوا يا رسول الله إنا نغسل الأدبار بالماء، وقال ابن جرير حدثني محمد بن عمارة الأسدي، حدثنا محمد بن سعد عن إبراهيم بن محمد عن شرحبيل بن سعد قال سمعت خزيمة بن ثابت يقول نزلت هذه الآية { فِيهِ رِجَالٌ يُحِبُّونَ أَن يَتَطَهَّرُواْ وَٱللَّهُ يُحِبُّ ٱلْمُطَّهِّرِينَ } قال كانوا يغسلون أدبارهم من الغائط. حديث آخر قال الإمام أحمد بن حنبل حدثنا يحيى بن آدم، حدثنا مالك، يعني ابن مغول، سمعت سياراً أبا الحكم عن شهر بن حوشب عن محمد بن عبد الله بن سلام قال لما قدم رسول الله صلى الله عليه وسلم يعني قباء، فقال " إن الله عز وجل قد أثنى عليكم في الطهور خيراً، أفلا تخبروني؟ " يعني قوله { فِيهِ رِجَالٌ يُحِبُّونَ أَن يَتَطَهَّرُواْ } فقالوا يا رسول الله إنا نجده مكتوباً علينا في التوراة الاستنجاء بالماء.

Abu Dawud narrated: ... the Prophet (peace be upon him) said: "This verse was revealed concerning the people of Quba (Mosque): {In it are men who love to purify themselves} — he said, they used water to cleanse themselves, and this verse was revealed about them." ...

Al-Tabarani narrated: .. "When this verse {In it are men who love to purify themselves} was revealed, the Messenger of Allah (peace be upon him) sent for 'Uwaym bin Sa'idah and asked, 'What is this purification that Allah has praised you for?' 'Uwaym said, 'O Messenger of Allah, none of us, whether man or woman, would relieve themselves without washing their private parts (with water).' The Prophet (peace be upon him) then said, 'That is it.'"

Imam Ahmad narrated: ... the Prophet (peace be upon him) came to them in the Mosque of Quba and said, "Indeed, Allah has praised you for your purification in connection with your mosque. What is the purification that you practice?" They replied, "By Allah, O Messenger of Allah, we know nothing except that we had Jewish neighbors, and they used to wash their private parts after defecation, so we did the same." This was also narrated by Ibn Khuzaymah in his Sahih.

Hisham narrated from Abdul Hamid Al-Madani from Ibrahim bin Isma'il Al-Ansari that the Messenger of Allah (peace be upon him) said to 'Uwaym bin Sa'idah: "What is this that Allah has praised you for: {In it are men who love to purify themselves}?" They said, "O Messenger of Allah, we wash our private parts with water."

Ibn Jarir narrated: ... 'This verse was revealed: {In it are men who love to purify themselves, and Allah loves those who purify themselves} — they used to wash their private parts (with water) after defecation.'"

Another narration: Imam Ahmad bin Hanbal reported: Yahya bin Adam narrated to us, Malik bin Mughul narrated: I heard Sayyar Abu Al-Hakam narrating from Shahr bin Hawshab from Muhammad bin Abdullah bin Salam, who said: "When the Messenger of Allah (peace be upon him) arrived at Quba, he said: 'Indeed, Allah has praised you for your purification. Would you not tell me?' referring to the verse {In it are men who love to purify themselves}. They replied, 'O Messenger of Allah, we find it written in the Torah to clean ourselves with water after defecation.'"

It is important to note that the incident of Masjid al-Dirar took place in the 9th year of Hijri, after the Expedition of Tabuk. The verse in question is found in Surah al-Tawbah, which was also revealed in the 9th Hijri year, just one year before the death of Prophet Muhammad.

Therefore, the objections are:

If the revelation had truly come from a 'All-Wise' (All-Knowing) Allah, it would have given logical and sensible instructions from the very BEGINNING, that cleanliness should be done with water, but if water is not available, then stones can be used.
Due to the seemingly illogical and contrary-to-wisdom manner in which the revelation was delivered, for 22 years, the Prophet and all Muslims continued using the unhygienic method of stones, even when water was available.

This proves that there is no divine being (Allah) guiding these revelations, and that Muhammad was crafting the religion on his own. Since Muhammad was only human, it explains the presence of such human errors within the revelations.

A Muslim Objection:

A Muslim wrote:

It is futile to debate the branches when there's disagreement about the very existence of the tree. We, as Muslims, believe in Allah's existence and in Prophet Muhammad as the true prophet. This leads us to the conviction that they are infallible, and anything we don't understand is simply a WISDOM beyond our comprehension.

Our Response:

The challenge with Islam is that the "tree" remains hidden. Neither Allah appears, nor do angels or miracles manifest. Islam instead asks us to observe its "branches" to recognize the tree.

However, when we examine these branches and find them lacking in wisdom, with human errors evident, Islamists then tell us to trust in the "tree trunk" and overlook the flaws in the branches, discouraging any criticism of these errors.

PS:

Islam rules to use a stone to clean the penis or vagina after urination when water is unavailable. However, this practice raises several concerns. Stones, being hard and abrasive, can cause discomfort or even injury to the sensitive skin of these areas. Additionally, stones may carry harmful bacteria or contaminants, even if they appear dry or clean on the surface, increasing the risk of infections.
In India, Hindus are found to be complaining that Muslims still often use stones (if water is not available) in modern toilets, and then throw them in the toilet, causing blockages.
In Europe too, people complain that Muslims wipe their penis with tissue papers after using urinals and then dispose of the soiled paper in the urinals, causing blockages.

Credit: Cuka-Blyat1234