Is my axie sick?

I have a wildtype axie who has developed all of a sudden darker pigmentation- such as under her eye- it looks like a black eye but has been there for about 6 weeks. Also there is a spot on her tail that used to be a sore that I treated, but now it looks like a darker patch- almost like scar tissue. Also, do axies bruise? because she has an area on her tail that is a purple colour, like a bruise- about 1cm long. Also- this is a persistent problem- every so often a few of the gill feathery bits goes black, and a new one grows. Is this normal?

There are two axies in the tank who have lived together for 3 years. They both are active and eat well. The water temp is about 15C-16C, pH is about 6.5; ammonia 0, nitrites 0 and nitrate about 60ppm- I just can't get it any lower. The tank is 3 foot- with lots of plastic plants, one piece of driftwood and a PVC hidey hole.

The tail may very well be scar tissue where you treated it - one of ours has a slightly ragged looking tail from where it was bitten off as a juvenile and how it regenerated. We have another dark wildtype that also has a dark oval spot above its right eye - definitely not part of the pigment as it looks slightly dented in but has had it for over 2.5 years, prior to us owning her - we've had her for 2 years (hasn't grown any and doesn't seem to bother it though we do keep an eye on it just to be on the safe side).