Continuity mistake: In the treasure vault Riley stands in front of that emerald statue, and on its chest you can see a part which is not covered in dust. In the next shot the whole chest is covered in dust. The clean area coincides with the later placement of Riley's cheek, which means the first shot was actually taken after the embracing and implemented before.
Revealing mistake: When Ben and Ian get the two different fingerprints from two different people, Mr. Ferguson [random security guard] and Abigail Chase, they are the exact same fingerprints. This can be confirmed on the DVD with pause and zoom. Moreover, the two scans show exactly the same emphasis/pressure on different regions within the print, with more light and detail on the left side and little in the center.
Factual error: In the scene when Ben, Abigail and Riley are on the tower of Independence Hall, they look at the shadow marking the secret place where the glasses are hidden. It is 3:20. The shadow of the cross is in the second third of the pillar. When Ian is on the tower the shadow has already moved to the top of the wall. As the others have left Independence Hall at 3:28 the shadow must have traveled the distance in about 4 minutes. This is far too quickly.