Continuity mistake: When Toad General calls for the council's attention and announces that Bowser found the Super Star, note his shirt buttons. Then, when he says that the Kongs will never agree because their mad king doesn't make alliances, Toad General's shirt is backwards, his buttons are on the opposite side. (00:24:55 - 00:25:35)
Revealing mistake: When young Indy jumps from his car to the motorbike and fights against a German - and the following scene where he rides on the bike towards the train - his body and especially his face are a blatant CGI creation with unnatural movements, dead eyes, and waxy, lifeless expressions (most noticeable in theater screenings). (00:05:53)
Continuity mistake: When Young Barry vanishes in the kitchen, the way his empty robe folds changes between shots. Also, the spoon falls on the robe but suddenly appears on the floor a shot later.
Continuity mistake: When the yellow car overturns, Isabel disappears. (01:06:50)
Revealing mistake: While inside the tunnel in Rome, before the yellow Fiat makes a U-turn multiple skid marks from previous takes are visible. Though one might pressume that the marks were already there, they are at the same spot and have the same pattern as the skid marks that the cars make seconds later.
Continuity mistake: When Hespera and Kalypso push the glass vitrine away, it falls and shatters into a zillion pieces. Half a second later, there's not a single bit of glass around. There's a better angle of the immaculate floor when a guard jumps on top of a woman.
Continuity mistake: Scott hugs his daughter and caresses her face while she holds his wrist. From the opposite angle, her hand is gone.