I'd catch it and do a freshwater dip for 7 minutes. If it's flukes, they'll peel off the eyes (and possibly gills and mouth) after about 4 minutes. It's important to leave the fish in the bath for long enough - in my experience it takes about 4 minutes for the flukes to die and fall off. Otherwise it's a waste of time. The flukes look sort of like translucent sesame seeds (similar size/shape). The change is osmotic pressure is too much for them and they die and fall off. Very common in angels, and a bit less often in tangs.
If nothing comes off after 4-7 minutes, then that pretty much rules out flukes and we're back to the drawing board.
Prazi-Pro is effective to treat as well, and can be used in the display (some risk to fanworms)... but the FW dip is a pretty fast way to know if that's what you're dealing with. Fresh RO water with similar temperature - some people take great pains to match pH (I don't.. but if I don't mention it somebody else will

) If the dip reveals that it is trematodes, then you may wish to treat the display to reduce the risk of reinfestation.
Quarantine is the best way to prevent this from getting into the display - but that ship has already sailed.
The "cyst" - IF it's lymphocystis, it will go away on its own when the fish no longer feels stressed, so I'd leave that alone. It's viral, and usually harmless unless it affects the fish's ability to eat, such as when it's on the mouth. If it's not impeding the fish in any way, let it be, it will go away.
Again - I'm guessing without the benefit of pictures, so take it for what it's worth.
Jenn