Plot hole: The famous line "There can be only one" is uttered in every Highlander film. At the end of the original, Connor obtained the prize by killing the Kurgan and being the last one. However, in this film and others, you find out that there are still others around, such as Duncan, the woman who was Duncan's girlfriend in Endgame, the other immortals following Jacob in Endgame, and the ones that showed up in The Source. So, why did Connor obtain the prize? He still wasn't the last one.
Plot hole: It's never really addressed or explained how Shredder survived his death in the previous movie from being crushed in a garbage truck.
Suggested correction: It didn't really need to be addressed, and thus is not a mistake. His hand emerging from the junkyard is enough to show that he survived his apparent demise at the end of the last film.
Plot hole: When Torch, Blade and Leech Woman go to the farmer and his wife's house while they are asleep, they killed both the farmer and his wife. The wife was consumed by flames, but not the farmer. When Torch and Blade returned to the Puppet Master with the brains, the Puppet Master says the brains are burnt up. The farmer's brain would not have been burnt up, only his wife. (00:31:50 - 00:37:50)
Plot hole: After Cali's father is killed the decision is made to cut power to the school so he or his men don't find out about his father. But if power was cut to the school then what is powering all the machinery in the kitchen that's providing food for 90 students?
Plot hole: In the first film, Toulon fled to America and, when the Nazis found him, committed suicide in 1939. But this movie, effectively the prequel to the franchise, opens in 1941.