Is it possible to get a picture? If not, what size are the spots?
Also, how old is the tank? Ive heard ammonia burns could cause that? Although i could very easily be wrong.
Also it is possible for it to be a colouration, despite it being a 'dalmation' molly. A quick Google search for 'yellow spots on dalmation molly' will show you what i mean.
Its not uncommon for fish to change colour shortly after purchase. But this doesnt mean you should just leave it. Be sure to check your water ammonia, nitrite and nitrate levels.
Also please bear in mind that mollys will only thrive in very hard/almost brackish conditions.