My first tank was a 55 and I had no clue about over stocking, over feeding, cleaning the filters properly.... I ended up with a bacteria bloom apparently but before I knew there wss an issue i bought more fish, I had 11 fish (a couple were goldfish too) in a 55 with a filter that was bare minimum for the size of tank..... the new fish I bought had ick (no knowledge of hospital tank) and so I had to treat the tank and took out the filter media to do so .... well with an over stocked tank and not proper media my tank for ammonia poisoning, it was horrible to see these fish go through this, luckily after 48 hours of 80%water changes 3x and then a full on swap of water and took all decoration, all everything out except heater filter and sponge filter and bubbler .... they all survived ... it w as s such a horrible thing to go throug, and nothing to do but wait and hope for the best.
I did not notice any "rotting" or holes in them but they also A ll survived.. ammonia poisoning can burn them though and if extreme enough I'm sure could cause flesh to deteriorate rather quickly.
Hope you get it figured out.
I now over filter my tanks! And do not over stock and I water change minimum 45% a week and I take my fish net and do the tornado in their tank every other day ( if needed) and clean up the bottom of any waste.