FBI: Here are your options. Door number one you go to prison for a very long time, door number two you help us get back the declaration from Ian, and you'll still go to prison for a very long time, but you'll feel good inside.
Ben Gates: Is there a door that doesn't lead to prision?
FBI: Someone's gotta go to prison, Ben.
As Ben is grabbing Abigail from Ian's vehicle, we see Shaw shoot at Ben and Riley's red van. He hits the top right corner of the sliding side door. When we see the side, sliding door again, there are no bullet holes, scratches, etc.
When Ben is talking to Riley in front of the Lincoln Memorial, you see a long pool behind them. This pool is filled with computer generated water, because the pool was drained at the time of shooting.