it is most likely that the bevel fixed it because it insulates the awkward topology on the top surface from the 90 degree corners. you could probably achieve the same result by insetting all the top faces.
re: small areas marked in blue, because these are just slightly inset, the AO is pretty weak here, but the inset cylinder goes way back, and settles on a dark gray color. IMO: these should have some nice fat bevels too for better readability