- Author Existence Failure : Mako Iwamatsu (Aku's Voice Actor), passed away in 2006, leaving The Movie in a bit of a lurch (especially since there were only two primary cast members in the first place.)
- Development Hell: The series was intended to end with a movie, but only in the late 2000s/early 2010s does it seem to be getting anywhere. Though people should remember that one of the main actors sadly passed away (Mako, who voiced the villain of the story, Aku). As stated above, his understudy Greg Baldwin would be a nice replacement.
- As the TV series has been revived for another season or more, this makes any film less likely.
- Name's the Same: Mad Jack is Jack's Evil Twin. There's also a boss in Donkey Kong 64 named Mad Jack, and a pirate named Mad Jack.
- Recycled Script: Most episodes are either about Jack attempting to find a way home, Aku sending a new assassain to kill Jack or finding a way to do it himself, or Jack finding some group of people oppressed by Aku's regime and helping to free them. It works in this case since the show really is more about fight sequences and strategy than storyline. And toward the end of the show, episode plots started to branch out more, with some new twists on ones that were already established.
Aku: Oh, put that thing away, Samurai. We all know what's going to happen. You'll swing your sword, I'll fly away, and probably say something like, "I'll be back, Samurai!" And then I'll flutter over the horizon and we probably won't see each for... about a week. And then we'll do the same thing again.Jack: Your word play will not trick me, villain! (Charges)Aku: (Transforms into a bat, floating away) I'll be back again, Samurai! You'll see! MWAHAHAHAHA! (Reappears) See what I mean?
- Screwed by the Network: When Samurai Jack was announced to making its return to Toonami, its timeslot wasn't revealed until a couple weeks before it actually returned, when it was revealed that it would air... at 4:00 AM. Granted, Samurai Jack is an old show at this point, but considering that 1) Samurai Jack hasn't aired on Toonami for about 6 years, 2) it was replacing FLCL (a show that is older than Samurai Jack, has been rerun into the ground on [adult swim] Action... and was airing at 2:30 AM despite these), and 3) 4:00 AM is the deadest hour of the night and is usually reserved for rerunning shows, it's still very disappointing. And starting January 31, 2015, the show will be removed from [adult swim]/Toonami entirely, as the block is losing the entire 5AM hour.
- Sequel Gap: The show got axed in 2004. Now in 2013 the series is finally getting a continuation through a new comic series published by IDW.
- Uncancelled: Late 2015, it was announced the series was being renewed and to air in 2016, 12 years after it ended.