When we are first introduced to Dr. Peabody, his shirt is pink, but when we cut to the examining room, his shirt is light blue.
Even though Junior threw away his polka-dot bow-tie in the final scene of the first film, he is wearing it again in almost every scene.
Previously, Ben was happily involved with Annie. Now he's single with no explanation.
Reflected in the window when Phlym holds Ben up against his truck.
Despite him and Junior being enemies in the first two films, Dr. Peabody doesn't know who Junior is, in this one.