I don't think there was a glitch for Toonz Premium. Somebody probably didn't calibrate the colors correctly when the episodes were being mastered. Krusty Love and Sailor Mouth are the only episodes I can think of that may have had a colorblind colorist, or there was something wrong with the computer monitor they used to color the episode.
Some episodes look normal when they have a clean copy, Band Geeks and the Secret Box look normal on their original prints. They only look bad when they're ran through Nick US, which has very bad dot crawl. Someone probably broadcasted them using composite. PAL region has scart which is why they typically don't look bad or have dot crawl in that region. Krusty Love, Gary Takes a Bath, Frankendoodle and Sailor Mouth have coloring issues regardless of the master. Episodes with slight coloring differences are a stylistic choice. Sailor Mouth and Krusty Love have the worst coloring out of any episode in season 2. Spongegaurd on duty and My Pretty Seahorse have very bland colors, same with Nasty Patty.