Looks like it's nothing that can't be sorted by adjusting the bridge saddle height. But just take the neck off (first loosen the strings and then put a capo on the first fret to keep the strings in place - or wrap some tape around the neck there to do the same thing - to save having to fit new strings) and check that there aren't any bits of wood or paint stopping the neck from sitting flat against the pocket. Just screwing in the screws can raise the wood around the screw holes, so smooth those areas down.

I'd also (if not like it already) widen the neck screw holes in the body only, so that each screw just fits in without touching the side. This allows the screw to pull down tight as it can on the neck without the screw first maxing out on the body section.