Visible crew/equipment: After escaping the T. Rex, when Alan and the kids climb the huge tree we can see a bit of what looks like netting at the top right side of the screen and also the set's scaffolding at the left side, then after the scene with Hammond and Ellie in the dining hall, when it cuts back to Alan and the kids we can see much more of the netting behind the tree set, at the top of the screen.
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)