The fact that he doesn't have toes/feet, most likely means that he was kept with other axies in a too small space. When axies are in a small tank with too many, they tend to bite each other, and that means that sometimes they lose a foot or a whole leg. It will regenerate over time.
Shopkeepers tend to put a lot of them in a confined space, because it is cheaper, but the axies don't apreciate it and can get agressive with eachother.
The gills are not thát much of a concern most of the time. As long as there are gill filaments on the branches they should be ok. I have an axie that has gills that are less then a centimeter, but she's perfectly happy.
If the gills were damaged in a fight or something, they will regenerate.
My experience with young axies is that they have enormous gills. I currently have 6 juvenile axies, and their gills are massive

.
A picture of the gills would give us a good impression if it's normal or not.
If your axie is morphing, what I doubt, it cannot be stopped.