Why did God answer the Prophet’s (PBUH) prayer for rain with water that caused the destruction of buildings and the drowning of property? And is it permissible to ask such a question?

The Prophet, may Allah bless him and grant him peace, was sent as a mercy to all creation. He responded to people's prayers for rain and for its cessation.

The mentioned hadith is evidence of his mercy towards people. It is possible that the Bedouin's statement about the destruction of property was an exaggeration of the abundance of rain or an anticipation of these damages, and the Prophet, may Allah bless him and grant him peace, did not intend that.

As for Allah's response to the Prophet's prayer for rain, that is because Allah does what He wills, and the Prophet, may Allah bless him and grant him peace, had his prayers answered, and because people were in need of rain.

There is no harm in this type of question if it is for learning or removing a misconception, and not for objection.