Hi ohaya,
All materials will go through some initial break in period and softening and change to some degree and the covers will also stretch and loosen to some degree as well. Latex will do this less than other types of foam. Softness and firmness is very subjective and the “feel” of a mattress when you press in with your hands is not an accurate test and is very different from the “feel” when you sleep on it. This is why you can’t test the softness of a mattress in a showroom by pressing on it with your hands … only by lying down on it.
It’s also possible that the mattress was “on the edge” of the most suitable softness level and that even a very small amount of change can have a more significant effect for some people (see post #2 here).
I’m not quite clear what you mean here by “top layer” but I’m guessing you mean the quilting layer and cover rather than a mattress pad or protector on the mattress or the top layer of latex?
Phoenix