Is it possible that if the (press in) wheel hub is a little offset the pressure from the caliper would not be evenly applied on one side of the caliper and would make noise upon braking?
First, what vehicle make model year WD and front or rear wheel?
Yes, in general it is possible that a hub that is not seated fully or true due uneven corrosion, will upset a parallel contact between the rotor and pad.
There's also other things that can cause noise, a hub usually isn't truly "press in", should still go in fairly easily and depend on the fasteners to hold it. If in doubt, maybe take it back off and wire wheel the (knuckle?) good.
If you had to use enormous force to get the hub in, maybe it was damaged doing so?