Looks like that doubler is supposed to be even at the top where the arrow points, but not even on the shoulders below that. I assume when glued properly the holes for the wing dowel line up. The reason they are not even at the shoulders is to follow the shape of the fuse. Personally I would just sand the angle into the shoulders then add a small piece of aircraft ply maybe (1" x 1") on the doubler, over the hole for the wing dowel. Then redrill that hole based on the hole in the former, NOT the doubler that you glued in the wrong position.

In the future you can insert a dowel into the dowel hole to make sure they line up while gluing.