I did some little discoveries regarding bad clones/the level 0 bad clones in pokémon Crystal. I hope they'll will help!
If your bad clone is making your box unacessible, you can enter in a wild battle, use your bike or a TM outside battle to fix this. I think it's because it uses data of the last action you did or something to put as his name. If you didn't do anything or spoke with someone as the last action you did before seeing it, the name will be a bunch of garbage, which causes freezing or the need to press A for a long time.
Regarding the lv.0 clone (the one used for celebi glitch), maybe his IVs all turn 0 or at least change from the original. The proof for that is that I cloned my red gyarados, and in return I received a level 0, blue one.