Kermit's hand shifts on and off the back of the bench between shots during Gonzo's song in the alternate universe
When Miss Bitterman is showing Pepe her Club Dot, her head changes position in front of the window between shots.
When the Boss magically changes Daniel's clothes, there is a brief gap that has been edited in another shot to create the illusion that Daniel's clothes have changed.
When Fozzie is painted green, he loses his hat, allowing for the fur on top of his head to be curled to a point to better resemble the Grinch. After he runs through the steam room and the paint dissolves, his hat is suddenly back.
As with all major Muppet productions, starting with Muppets from Space (1999), the arm rods for the Muppet characters (used to move their arms and sometimes other extremities), have been digitally removed. However, the rods can still be seen in several shots, mostly involving Rizzo and Kermit. Rods can be seen on Rizzo after he slams into a wall, on Kermit when Daniel finds him frozen on the bench, on when Kermit is in Miss Piggy's apartment in the alternate timeline.
In the final fight between Miss Bitterman and Miss Piggy, Mr Bitterman can be heard saying "Do you want a piece of me?" The camera cuts back to her just before 'of me', and her mouth is shut. Her next line is "I see you are very agile for a plus sized pig!" However, her mouth movements suggest that the original line was quite different - she appears to be saying 'oink oink oink' at the end of her line - and the final line has been clumsily overdubbed.
In the alternate world where Kermit wasn't born, Robin is somehow present in the Dot nightclub. Without Kermit, Robin wouldn't exist either.