This is a good idea, let's talk about specifics. So two groups of minions would potentially not get along well, and given some low morale, they could start fighting.
What would be the trigger? Big enough number of both groups in the same room? Or a goblin walking into the graveyard and waking up a vampire?
How would you prevent this situation? Have them live in different parts of the dungeon? I guess it would be possible to designate that such and such minions train in this training room, others in another. Another option would be to lock off trouble making minions.
If they start fighting, what would happen? Would they fight until one of the groups is all killed or stop and be peaceful again after 2-3 kills? As a player, what could you do? You can't pick up minions like in Dungeon Keeper…
This kind of thing is easy to add, once I (or you) have all the mechanics figured out, and have some certainty that it will positively impact the game (I'm not sure yet).