Pictures would help (of living or dead).
Off the top of my head, it sounds like flukes aka trematodes. These parasites typically infest the eyes, mouth and gills first but may spread to other areas. They are about the size/shape of a sesame seed, and are sort of translucent. When they infest the eyes they cloud them over.
They don't kill directly - rather, in severe infestations they impair the fishes' ability to breathe (and see, and eat). Also a risk factor is a secondary infection from the bite sites.
We see them most (and first) in tangs and angels, although any fish can be affected.
Quarantine and treatment with PraziPro will kill the flukes. You can also do a freshwater bath for 7 or so minutes if you're brave enough to try that. It's not a difficult procedure - the hardest part is catching the fish to do it, but often times it's as stressful or more stressful to the hobbyist as it is to the fish.
The parasite can't handle the osmotic shock, dies and falls off.
PraziPro can be used in a reef setting. It's contraindicated where fanworms and similar are present, and you would need to remove carbon and turn off your skimmer for at least 5 days.
Treatment in a quarantine tank is always preferred, but PraziPro *can* be used in the display with suitable caution.
I'm not 100% sure that's what you've got going on, but based on your description that's my best educated guess.
Jenn