Plot hole: When Dr. Marvin is trying to get Bob to leave the night before his television interview, he can't leave because it's pouring rain. He also can't drive him because their car was left at the boat dock. However, Dr. Marvin could have easily called for a cab to drive Bob back to where he's staying.
Suggested correction: This assumes that there is a taxi service in the small town in which they reside.
This is obviously a tourist town, which would likely create the need for a taxi service.
It also seems to be a fairly secluded and very rich tourist town with cars almost necessary to get around.
Suggested correction: At that time of night in that condition, I highly doubt calling a taxi cab would be easy, especially since Bob lives right down the road, no taxi far away would come just to drive someone a short distance like that.
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)