I suspect there were some loose eggs in with your super worms that developed later. I wish it was that easy.
They pupate in separate containers because they are canabalistic and are helpless in that stage. Warmth makes them pupate faster. The beetles do better and lay more eggs if you keep them very warm.I have been trying to breed these beetles and it has taken quite some time to get even the small colony I have (20) they die off pretty quick and they dont pupate that fast, still have not seen any babies, going on 3 months now, and correct these worms need to be stressed out and by themselves in order to change to beetles, they are a social colony and won't change,it is almost impossible to breed these worms without pupating fist. horn worms change into moths and wax worms.