Hey SC, while I check to make sure frets are smooth with each kit, I’ve seen this happen and yes definitely humidity could be a factor.
I would sweep a file along the edges of the fingerboard. Then go over with around 150 grit sandpaper and continue through to 220 and 320 as you sand the rest of the neck.
I imagine the wood has shrunk as much as it is going to and once you seal it with a finish, varnish, oil etc, it will be pretty stable.