Tank looks over crowded. Your fishes skin is being irritated by bad water quality. If you havent disconnected your filters when treating this tank for parasites you most likely wiped out the beneficial bacteria residing within. An easy way to stop the puffy growths on your fishes flanks is keeping the PH well over 7, and 70% weekly water changes. When water is being returned to your tank make sure to have it bounce off a rock or wood. This helps displace the chlorine which benefits the fish when doing large water changes. No chemicals are needed. Just use kosher salt for the first few water changes and reduce the amount of food used when feeding. This will allow the bacteria to build up again. Certain fish are more prone to be effected by bad water quality than others. As a matter of fact, your water quality may be perfectly fine for the RTMs but not good enough for Bifasciatums and Carpintes. This is why you can allways expect to find hardy fish at the shop like Oscars, Convicts, Red Devils and Pacus. But fish that are not so hardy ie; Altums, Carpinte, Rivulatus, and most Geophagus are found ocassionally.