There are fans that reject the sequel series Ben 10: Alien Force (and, in turn, everything after) due to the numerous retcons it made; the two most egregious being Gwen and Kevin's powers being made alien in origin, rather than magic or natural mutation, and immediately turning the latter character into a good guy without the presence of a redemption arc.
There are fans of the first three series that don't consider Omniverse canon note Or at least everything after the first two episodes, which were written by previous showrunner Dwayne McDuffie due to its change of tone, character redesigns, and heavy use of comedy. Gwen fans in particular were especially divided with her new design: some thought it felt like a more like a natural evolution of her original series design, others disliked that it moved away from her AF/UA design as a consequence, and others just thought she took a dive in attractiveness.
While enjoyable episodes, some fans dismiss the episodes "So Long, And Thanks For All the Smoothies" and "Universe vs. Tennyson" due to the former ending with Ben being forced to recreate the entire universe after it was destroyed, as it implies that everyone except him died and have been replaced with identical copies and the latter revolving around Ben being put on trial for committing the act.
Some Omniverse fans don't consider the story arcs that followed after the first two and a half seasons as canon, simply because they feel the villains that followed were introduced paled in comparison to Khyber and Malware.
Fans of Helen, Manny, and Alan disregard the Voodoo Shark twist in the Season 6 episode "The Rooters of All Evil", which reveals that they're actually humans who were experimented on and given alien powers, rather than being Half-Human Hybrids. Some fans who came to like Kevin as a good guy would also disregard the controversial Retcon in which his father was never a Plumber as canon.
Even those who aren't fond of shipping consider the confirmation that Ben and Kai are the Official Couple non-canon for a myriad of reasons, ranging from dislike of the character herself and to Ben being viewed as having better chemistry with other characters like Ester or Rook. It doesn't help that the character's return after being absent throughout both Alien Force and Ultimate Alien was part of the show's goal to set up the future of the original series episode "Ben 10,000", which was meant to be an Alternate Timeline to begin with.
