Hacked moves shouldn't affect anything, I got a Victini with V Create, Fusion Bolt and Fusion Flare (one an event Signature move, the other two being moves of Other pokemon) because, really, event pokemon (even ones given out by Nintendo like the movie Victini) given out with moves they shouldn't know are, basically, hacked. They're moves the pokemon can't learn, so you shouldn't need to delete them, as my Victini didn't need to have any moves deleted.
So to the people that have legitimate pokemon (that they're SURE are legitimate, as in they caught them themselves) are you contacting Nintendo/Gamefreak/TPC to report these? Sure you may not get a reply or help with your particular instance right away, but if enough people are reporting the issue, they could likely fix it eventually, but they won't fix something they don't know there is a problem with.