I'd suggest looking into Pokegen. It can actually make legal looking pokemon though I don't really use because I breed and all that jazz. Also, just uploaded a battle with someone else so I can assure you the problem was off on your end almost 100%. :V
If you ever get it all legal looking feel free to ask me for another. It was a fun battle.
Yeah, it's weird but that's the only thing I can think of other than my Victini. I got my Victini from a trade online and he assured me it was legal and I put it through some checks and made sure it was legal as well but I haven't gotten to formerly check it on GTS because event legendaries aren't allowed. :V
Lol, the button misclick at the end of the FC made it an 8 instead of an 9 apparently. That's why I deleted the post right after. Either way it was a good game dude. That crit almost cost me the match though which wasn't cool.