Well during the traditional-animated saga (2-6), there was the occasional moment when a little bit of colouring goes wrong, such as the yellow on Spike's beak/lips suddenly disappearing, or when Ducky's little horn suddenly going a really dark green colour. But, among outsourced traditional animation, such mistakes were pretty common, especially when on a low budget
Also, I do recall in number 9, during the shot of Cera and her dad pushing the log, if you look at the top of the screen, you can see some branches of the log sort of disappear. I say sort of, because it's not like they vanish completely, it's just that they were apparently supposed to go offscreen, but were a bit too low down, and so look unfinished instead.
And of course, there is that oft-mentioned shot in number 12 where the whites of Cera's eyes suddenly go electric blue for no reason. Check out her "Things Change" number. At the shot where she aproaches the stream, then climbs up onto the log across the stream, for the duration of that entire shot, her eyes' whites go bright blue. It's really weird because it stands out like a sore thumb. It's a real shame because it draws all the attention of an otherwise pretty powerful number.