It is most likely a direct cause from the ammonia/nitrites, but the symptoms are that of a parasite called Brooklynella hostilis. This is also called "clownfish disease/malady". As this is a possibility and it is contagious to other fish, you need to leave your tank fishless for a period of no less than 4 weeks.
More info on Brooklynella >>here
You should also be quarantining all your fish, more info on quarantine can be found >>here
Information on cycling without the use of live fish can be found >>here