Just found a glitch. For real this time, not just playing at 3 am and thinking everything was a Pokeball.
If you change the order of a Pokemon's moves while viewing their contest effects, the order will not save once you leave the status menu. I thought my game was defective or something because when I was in contests all of my moves would be in the wrong order. I just accidentally changed the order of them in the contest window while raising a Sableye and it happened again when I sent it out. Just tested it multiple times and it kept working.
Doubt it's anything dangerous, but at least now I know my save isn't corrupting.