I can think of two stupid things that I thought.
1. In the opening scene when Bonasera is asking Vito to avenge his daughter, when Vito says "Bonasera, Bonasera," I didn't realize he was calling him by his name, I thought he was dismissing him by saying "Buona sera," meaning good evening.
2. When Moe Green says he "made his bones" when Mike was going out with cheerleaders, I didn't know that making your bones meant killing someone...I thought it was some kind of sexual reference.