In The LEGO Movie (2014), the Swamp Creature was one of the Master Builders. However, in this film, he's in the Phantom Zone. It's doubtful that a Master Builder would go about committing crimes punishable by banishment to the Phantom Zone.
When Batman is returning to the phantom zone he is floating up at an angle away from the other characters but when he hits the barrier he falls straight down to be caught by Batgirl instead of landing much farther away.
The goof items below may give away important plot points.
When all the villains Batman recruits come to his aid, Scarecrow says, "We saw your signal, and we came to help!" This is exemplified by his body movements, making it obvious he's the one talking. However, the voice is completely different from Scarecrow's voice throughout the rest of the movie.
during the sequence when Batman & friends are trying to repair Gotham by bridging the crevices using themselves connected from head-to-foot, and trying to convince Joker to join them, many of Gotham City's villains, who were already shown to have previously put aside their differences and joined up with Batman, are now standing behind Joker on the other side of the crevice from Batman & friends, inexplicably doing nothing instead of trying to help bridge the gap.
Earlier in the film Superman sends Zod to the Phantom Zone but when Joker goes there he is nowhere to be seen. Many assume he doesn't return throughout the rest of the film. However, he does appear multiple times when Joker returns to Gotham with the villains from the Phantom Zone, albeit not as prominently featured.