Besides any specific bonus events like the "Bonus Room" where 6 or 7 Innocents appear at a time.
If you put Innocents into an item and go into the Item world, on random floors those Innocents will show up to be subdued. If there is no Innocent on the item (from either being removed or just never existing) will they continue to show up anyway, just as a random job as opposed to the ones you put there.