This is really not that big of a deal as long as the dowel is long enough to go into the hole.
What is important is to make sure the final wing mounting is as square to the fuselage as possible.
You will need to collect some information, this is just so you will know where the problem originated from, it won't affect what you need to do to fix it (unless you intend to tear the plane apart which is not necessary).
Get a small square and see if the former where the wing dowels mate is square to the fuselage on both sides.
Check the former at the back of the wing saddle too.
Check to see if the leading edge of the wing is straight. Maybe the leading edge was sanded more on one side than the other or when the wing halves were joined there is a small misalignment.

Using the center of the back edge of the fuselage as your reference set the wing in the wing saddle (dowels in the holes) and adjust the wing so the trailing edge of eacc wing tip is equal distance from the reference.
This will align the wing to be 'square' to the fuselage.
You will now drill the wing bolt holes so this alignment is maintained.

If the gaps (where ever they may be at this time) bother you, just glue in some scrap balsa and sand as required.