Its is easy for the arrival of fry to sneak up on you. They start to grow and suddenly their ammonia output is higher than realized- but testing should catch that.
I can't recall what diseases might cause patches and gill related issues. I am lucky in that my disease experience is somwhat limited on a 1st hand basis. I often rely on more expert folks for help myself. The things i have treated i know, the ones I have not i only know about or where ti find out about.
It is also possible you are seeing two different things. Salt wont help with ammonia only nitrite- or fungus and certain external parasites.
Its the operculum issues that bother me. I would treat the tank for flukes- QuICK Cure or Prazipro- to be sure.
For QuICk Cure- Do not use on: baby whales, elephant nose, shrimps, snails, living rock or invertebrates. Prazi is the way to go bu more money.
Salt dip would kill fluke on a fish but not free swimmers in tank- think ich like.