As far as I know Missgno can't corrupt your safe file. Some other glitch pokemon can, but none of those are encounterable without modifying the game data in some way. The worst Missigno does is corrupt your Hall of Fame data, but that has no effect on actual gameplay.
![TIMETHAI - ไม่อยากให้เป็นเขา (Why tho?) [OFFICIAL MV]](http://i.ytimg.com/vi/o2qYlGVVtOw/mqdefault.jpg)
Nintendo: hey dont do this
Every child ever: i'ma do this
MUST. BREAK. MY. GAME.
As far as I know Missgno can't corrupt your safe file. Some other glitch pokemon can, but none of those are encounterable without modifying the game data in some way. The worst Missigno does is corrupt your Hall of Fame data, but that has no effect on actual gameplay.