I've tried loading up Melee god knows how many times today and every time I get that same message followed by Dolphin crashing. Can someone PLEASE tell me how to fix this? (btw I'm running Dolphin 5.0-12247 and the game is in .nkit.iso format)
It's probably because you're using the nkit format. The nkit format is/can be a lossy compression format and introduces a lot of problems and it moves data around in the file. This causes a lot of problems for Dolphin that expects data in games to be in a certain spot.
You should redump your game, and if you're looking to compress your game to save space you can use the lossless RVZ format that Dolphin recently implemented.
While the NKit format can cause problems, I don't really see how it could have caused this specific problem. I'd rather suggest trying different graphics backends.