Plot hole: The assassin cuts a hole in the glass to kill the Federation president. But with the size of the hole and the placement of the scope on the phaser rifle, the assassin would not have been able to see out of the hole.
Plot hole: The helmet design is rubbish. The eyeholes are far too small - that close to the eyes the divider between the eyeholes would block almost a third of the wearer's vision. He would hardly be able to see what was right in front of him - and it is not too close nor too narrow to fall into the "blind spot" between the eyes. This is not a character error by Peevey - the helmet design came from the original plans - it is even shown in the German propaganda film!
Plot hole: At the bar shootout where everyone except Marlboro and Harley are murdered, the two jump through the window, over the fence, into the airport, and into an airplane luggage compartment. They would have been caught by security. The missing, and dead, airport worker would have been missed and searched for, the gunfire would have attracted attention, and the police would have been called. They never would have left the airport.
Plot hole: Throughout the movie, the strength of the two beasts fluctuates heavily; they can chew and break telephone posts with ease, they can toss a Turtle many meters in the air through a roof, but they are caged by makeshift cells of junk poorly pieced together or a little horse trailer. (00:39:30)
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: 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.