Disowned Adaptation: Rob Tapert openly hates the Dynamite Comics arcs, which act as a Fix Fic to developments that Tapert supported and continually defends to this day. One interview also suggests he's annoyed that Dynamite simply procured the licensing rights and didn't request any consultation (as he makes a point of criticizing them for doing that with their Army of Darkness comics).
Dye Hard: Lawless and O'Connor are both natural blondes; Lawless dyed her hair black (on Hercules) then brown, while O'Connor dyed hers red for most of the show's first two seasons.
Flip Flop of God: Ongoing after the show ended. Mostly regarding the nature of Xena and Gabrielle's relationship. Of note, around the time of the finale, Lucy Lawless felt it was "more than friends" due to a particular scene. By the time of recording DVD commentaries, this opinion was reversed.
What Could Have Been: A version of the script for "The Furies" would have revealed that Ares was indeed Xena's father (this was changed due to 1) not wanting Xena to be a half-god like Hercules, and 2) the Squick factor that would result from Ares' constant interest in Xena). The final version is ambiguous enough that some people assume this to be the case anyway.