Did the spots show up suddenly? If you aren't sure, do you have any older (but not *too* old) photos that you could check? It's a little hard to tell what's going on with the patches because of the lighting (but lotls are pretty hard to photograph). My little lotl, a few months old at most, has some sort of similar-looking spots but I'm convinced in his/her case it's just natural coloration.
Slime coat seems like a potentially likely factor, if it's thick or thin in one place and causing a bit of a sheen.
But yes, as everyone else mentioned, the gravel has to go immediately. A bare tank bottom is fine, so no need to wait until if and when you find a replacement substrate! Those rocks look delicious, and if I might eat them, she might too.
Relatedly... after you get the gravel out, keep an eye out for poo! I think axolotls' metabolisms vary, but if she keeps making a good loaf here and there, that'll help ease any worry that she ate a rock before you got them out. If she stops, come back and ask for advice; everyone here talks about poo.