PokéBase - Pokémon Q&A
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Sometimes switching a game on and off will solve the problem, depending on how serious/ what the glitch is, but for the most part you'll need to restart your entire game (e.g. if you get a bad egg; AR codes will cause this and many other problems in your game).

Best way to prevent all of this? Don't cheat.

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can PokeGen cause Glitches/Hacks ?
Yes. Tampering with your game in any way will result in possible glitches. That's the risk you take when you attempt to edit/ change your gameplay through non-intended methods.
but PX said it is safe
I've had friends who have ruined their games via editing their games, PokeGen and all.

Perhaps they were using other cheats too, but PokeGen uses AR codes too, and AR codes are always liable to glitch up your game.