Continuity mistake: When both Explorer vehicles are parked at the paddock, in the shot of the goat being raised to lure the T. Rex, the "No! Feeding..." sign is permanently affixed to the front of the concrete wall, but in the previous and following shots that same sign is affixed to the angled top part of the wall. Later, when the power goes out, that sign is once again affixed to the front of the concrete wall.
Visible crew/equipment: When Benedict snaps his fingers and the dogs form a pyramid to show how well they are trained - look at the dog's feet and you can see the rails that the dogs are standing on. (00:43:50)
Continuity mistake: At the beginning, when Rochefort walks out onto the balcony to address the Musketeers in the courtyard, the guard on Rochefort's left obviously changes halberd/pikes between shots as they are completely different. (00:08:20)
Character mistake: When Mario and Luigi are escaping in the stolen Police car, a warning on their screen reads "Tunnel not finnished." (00:43:30)