I had a couple of folks PM me because they didn't understand the square peg/round hole thing, so just in case anyone else is thinking what is she talking about, but are too polite to ask....
Tony is trying to fit the square peg (EJ) into the round hole (the Ziva shaped hole in his life). Not a good fit, but he was working on doing it because he was working on getting over Ziva - EJ is a ill fitting substitute for what is meant to fill that hole in his life (Ziva) - thus his irritation with Ziva - she is undoing all the work he thought he had accomplished.
sorry, it wasn't clear - I was trying to hold myself to 100 words.