The 'missing' shoe.

I think you're right. The shoe wasn't actually contacting Costigan's hand. That was pretty noticeable. I guess DiCaprio (the little prima donna) didn't want to take a chance of getting his hand hurt.

I never had to watch closely because I noticed it right away. Alright maybe the second time around, lol. It’s off-putting yet hilarious.

So why in the world did Scorsese let it go? Maybe because once he noticed it he decided to let this moment be The Departed’s Sonny Corleone beating scene in The Godfather (you know which one). Or he felt he got the perfect shot with the actors, who knows.

And Leo too afraid to take a chance at getting hurt? I guess him and nearly every non-method actor. Although, if he was supposedly as desperate for an Oscar back then as he was for the next 8 years (that was fun), then not for a second would he had hesitated to let Nicholson bust his cast arm for real. In fact, he would have demanded to do as many takes as possible until they got the right shot. :D

There are a few times that editing didn't catch things. There was the scene where the police and Costello's men both meet at the Washington Street building, and end up in a shootout. As the thugs speed away in the van, you see a closeup of one of the van's back windows get shot out, that it pans out and you see the other window get shot out, than the original one shot out again.

I never got that scene anyway. I understand them smashing the cast to check there's not a wire underneath.
What I don't get is why they then start bashing his injured arm with the shoe. What's he gonna say "damn, you got me. OK, I am a cop. Now please continue with this torture until I die from it".