If you know of any, post them in this thread. I have a few gems already in mind. Even better if you have links to those posts.
One I remember is a complaint over Mavado's Red Dragon symbol, thinking it was akin to palette swapping since it looked exactly like Kano's symbol only red, and who feared that people who hated the palette swaps ninjas were gonna throw a fit. Holy hell. Yes, identical logos on two characters who otherwise look and act completely differently from one another is the exact same thing as a palette swap.
Next is about the DC crossover, when it was in development. There was some poster who was afraid that "in-fighting" (as in, MK characters vs MK characters or DC ones vs other DC ones) was going to be impossible, and I think it's because screenshots of the game back then only showed crossover fights. Ha ha! Of course they were primarily showing crossover fights, for commercial purposes, since the game's title was MK VS DC Universe! Not MK vs MK or DC Universe vs DC universe.
Another, once again involving the crossover, was this obsession with "fitting" matches. I believe it was known that the Joker would fight Kano in the story mode, and some twit who didn't think these two were fitting rivals was trying to think of similarities between the two that would justify such an encounter. Like characters in the story mode could only fight their rivals, or something.
To conclude, there was this dumb theory of Drahmin being Kabal. No doubt since they're both disfigured and cover their faces.