I've been doing a few any% Sick runs on THUG 1, and I've noticed that the last mission is skipped most of the time, but every run I've seen still does the mission. Is this some glitch that not allowed in a run? If so, how can I stop it from happening?

This occurs because you have a previous save file in which you saved after you beat the final mission in the last chapter. We consider an any% run as a run in which you complete the Eric mission. So in order to avoid the last mission skip you need to clear your save file and not save after chapter 27 from here on out(for pc) or clear your data each time you do a console run... Or just go back in the game w/ "continue story" and either skate to the goal or select it from the menu depending on what category you're running.