can mystic swordsman lv 2 stop apprentice magicians effect from going off

If Apprentice is face-down, yes it will.

What deck wraith said. When MSLV2 attacks a face-down it uses its effect, in which case apprentice would be considered destroyed by the effect and not by battle, so its effect would not be triggered. Same reason why you can't level up MSLV2 after using its effect, it didn't destroy a monster "in battle".

yea, i remembered when i had the mystic set and i was like, attack f/d, then level up to 4, when i was told i couldn't i was like, WTF? i was new to yugioh then lol. but still, after that, the mystic's came out indefinitly *well, 4 and 6*