Plot hole: While on the boat, Paddington suddenly appears inside the mail sack, thus implying he managed to open the precinct, get inside the sack and find someone who closed the precinct again. An impossible task.
Plot hole: In Night at the Museum 2, the parts of the tablet that are missing were attached to the gate to the underworld, which implies it was originally attached to that, and those parts were left behind when it was removed. But in this film we see the tablet getting found on the wall in Ahkmenrah's tomb, and the missing parts are left behind on the wall of the tomb.
Plot hole: After Hannigan feels guilty for what she did, she confesses to the girls, and they find Mr. Stacks to tell him. The fact is, they went straight to where he worked - but Annie never told them the destination, and Guy himself never told Hannigan where it was either. So, how did they get there, and most importantly, know where it was?