who filled the hole in the tree and why?

It is clear enough that Boo Radley is the one leaving them gifts. They are both so curious about his life, and try to pass him messages through his house windows, but are reprimanded by their father. They don't know for certain that Boo is sending the gifts, but when they go one day to try and communicate with the gift-giver, they find that Boo's brother has cemented the hole. He is the same one who fires a gun to keep them away when they try to pass messages, and it's more evidence that Boo was the gift-giver.

Oh, and the implication is Boo's brother filled the hole so as to keep the kids and Boo from communicating.