You can't know for sure due to the unpredictable nature of hacks and glitches, but assuming that you are playing a Gen 6 game, the chances of anything bad happening as a result of hacking (or receiving a hacked Pokemon) is very low. The games deal with hacks and glitches much better than the older games do.
Based on the lack of information on Bad Eggs in Gen 6 on Bulbapedia, they're quite rare. Not much is known about how you can get one. You should be fine.