5. The Mac OS/Alien Mothership Debacle - Independence Day
The Confusing Moment:
It's pretty infamous by now, but how did David Levinson use Mac OS 7.6 to upload a virus to an alien mothership? The compatibility issues alone are staggering, considering you can't even get Android and iOS to play nice most of the time.
The Deleted Scene:
Levinson's virus was not an accidental discovery or a hack that came out of nowhere. In the original cut of the movie, he actually gets taken to see one of the alien crafts inside Area 51 by Dr. Brakish Okun, where they discuss the technology and David seemingly breaks their technological encryption (based on the same sequential reference point he used to decipher the countdown).
In this case, the deleted scene was actually the right cut to make, because it's horribly boring and kills the pace of the movie. It's just a shame that the whole plot point would then go on to become some sort of flag-bearer for idiotic movie plot-holes for decades.
The scene can be seen from the 05:58 point in this compilation...