MST3K Mantra: Since there were so many problems with production, the movie relies on the mantra a lot to make up for the plot holes and lack of continuity. As The Agony Booth pointed out, if a movie is so full of plot holes that you have to be completely stoned just to enjoy it, then it's not a good movie.
Nightmare Fuel: B-17. The shortest segment, but definitely the one that accomplishes its goal for the largest portion of the audience, and that goal is to be fucking terrifying. Whether it is the opening section where most of the bomber crew is killed in a difficult bombing run or the Zombie Apocalypse afterward is a matter of opinion.
They Just Didn't Care: For whatever reason, the final two scenes of "So Beautiful, So Dangerous" are hastily edited together in reverse order. In the final cut of the film, Gloria and the Robot get off the spaceship and walk onto one of the space station's escalators[1], followed by Zeke and Edsel landing the ship on the station. Once again, try not to think too hard about this.
↑You can even hear a tiny bit of Elmer Bernstein's end-of-segment music a split second before "Heavy Metal" by Sammy Hagar kicks in, meaning they had it correct at one point in the editing process