Assalaamu alaykum. There is a hadith that says that Ibn ‘Umar, may Allaah be pleased with him, used to throw pebbles at people who did not perform Raf'ul-Yadayn (raising hands before and after Rukoo' [bowing]) in the prayer. Did that not cause a disturbance in the prayer?

All perfect praise be to Allah, The Lord of the worlds. I testify that there is none worthy of worship except Allah and that Muhammad, sallallahu ‘alayhi wa sallam, is His slave and Messenger.

What you mentioned about Ibn ‘Umar was cited by Al-Bukhari in the part on Raf'ul-Yadayn in prayer, and it is not problematic, praise be to Allah. The report does not say that Ibn ‘Umar used to do that (throw pebbles) while he was praying. Rather, it says that when he saw someone performing the prayer and not raising his hands before and after Rukoo‘, he would throw pebbles at him. Apparently, he did that while he himself was not praying, so there is no problem here.

However, if you are asking about the validity of the prayer of the person at whom the pebbles were thrown, then you should know that what Ibn ‘Umar did does not invalidate the prayer nor affect its validity. He used to do that only to alert the person that he was leaving an act of the Sunnah. It is also apparent that he did not throw them in a manner that would harm the praying person; rather, it was only to alert him. Such an act does not affect the validity of the prayer, as we explained.

Allah knows best.