The first "mouse clip" in the Mouse music video (not counting the flashcard) is not a mouse at all. It's a pika, which is related to rabbits.
In the 2004 releases, the page transition from the "mouse" drawing to the "cat" drawing is blue, and the transition from the clip of Tyler playing with Joyful Puppy to the "cat" drawing is red unlike in 2001-2003 releases where it's white.
In the original 2001 release, the Crystalite Cat Mobile and Dotty Ladybug clips were exported in 30fps, but in the 2004 release, they were exported in the fixed 60fps.
In the 2004 releases, the puppet show where Pavlov sees bird footprints and pops up inside the nest shows the light switch in the background. It is currently unknown why it was removed in the 2001-2003 releases and then oddly added back in 2004.
In the original 2001 release, In the 1st clip of the Mouse Trap game, You can see the reflections of the black backdrop and the studio lights from the reflective ball.
During the puppet show where Pavlov wears a Rabbit Ears Headband and hops around, Markie Scholz's head is visible for a brief second.