Can you tell us more about the system, if you cycled your system, and how long you've had the fish?
It sounds like it could be ich, which would mean needing to treat in a QT/hospital tank with either hyposalinity or a copper based medication for 6-8 weeks with the display tank fallow to prevent any further infestation of ich.
You only see one of the life stages of ich. The others, where it is living in the sandbed before maturing and swimming up to find a host, can't be seen by the naked eye. I would still suggest treating like I already mentioned as I would bet you'll be seeing those spots again.