As Torno closes a sky light window a mark can be seen on it. Nick shoots, Torno ducks and it can be seen clearly that the mark is actually a bullet hole which shouldn't be there at that time as when Nuck fires a second time there's a slight puff of smoke from the hole and the sound of breaking glass.
The collar Father Jesse wears is not a Roman Catholic clergy collar, but a Protestant version.
The Bible passage Raft reads aloud is from Romans, the sixth of 27 books in the New Testament. Yet the Bible he holds is open to a page just a few pages before the end.
The check Johnny writes is dated 14 August 1946, but he's already been seen driving a 1948 Packard convertible.
Rocky fears that the clue in the Bible will implicate him, but this makes no sense because he is a stranger to the victim. Late in the movie he says, as if it is a sudden realization, what he knew all along--that the victim did not know his name, and therefore could not have left a clue to it.
When Det. Strecker pulls up at the trucking terminal to see Johnny (about 1 hour into the film), a clear reflection of the boom microphone is visible in the police car's windshield.