You put your fish in time out if they cause trouble? I'm sorry, but that is probably why you may have ich...
It is wide spread in all freshwater fish but appears to be more common in aquarium fish, possibly due to the closer contact and stress involved with aquarium species.
There are many causes of stress in a fish's life, many of which can be made worse or better by the owner. Water temperature, water quality, tank inhabitants, improper diet, and a variety of other factors all contribute to stress.
Your females most likely don't want the male hanging around, nor does the male want a "harem" of females flustering about. Seperating them into a breeder cup that stays in the aquarium for a "time out" is most likely stressing them out even further.
I'm not calling you a bad fish parent... just... they can only tolerate being in the same tank for so long, then they will turn.