If the plant is growing well, I think don't worry about it. Did you cut those leaves or did they fall off? I have had Masdevallias that seemed to be doing fine, then just dropped all their leaves and expired. I hope that's not what you are seeing. I would not cut leaves! I would consider the spots harmless.
Is your water quality good? Mine has dropped a few leaves and I think it can be a combination of heat stress together with low humidity winds and heavily mineralized water.
I have only been growing masdevallias for just under a year, but I also have some with yellowing leaves and leaf drop. I am thinking and hoping it is due to senescence as more growths and even a few spikes are pushing up. I don't cut them though, just wait for them to fall off with the presumption that the plant is pulling back whatever nutrients it needs from the leaf.