In the 2004 release during the Deep Blue Sea scene, there a minor glimpse of the original release's page peel transition during the first verse of the song after the turtle picture.
Also in the 2004 release, at the end of the savannah puppet show, Jared Picune (the editor for the 2004 re-releases) forgot to freeze frame the clip, resulting in viewers seeing Georgia Giraffe return to starting position in a fast swoop.
If you will look closely at Jane when she pulls the string to reveal the picture of the jungle, you can see her puppeteer's head pop up for a brief second.
During the Banana Split puppet show with Jane and Murray, one can see Mark Burr's shirt in the top left corner. In the 2004 release it is unbothered with and clearly visible.