What is the ruling on throwing the pebbles if some of them did not fall into the designated basin for throwing due to overcrowding, knowing that the pilgrim believed they had fallen into it?

If the thrower is certain or predominantly believes that the pebbles have landed in the target, then doubt after that is not given consideration. Doubt after completing an act of worship is not heeded; it is from the whisperings of Satan. Imam Al-Shafi'i differentiated between doubt during an action and doubt after an action. He did not mandate repeating the latter to avoid hardship.