This can happen, its not unheard of, I get it occasionally when I creating character heads - if you have a crease after merging. basically move the verts until the crease is no more - its that simple - you could use the artisan tool too to smooth it out.

you could also do an instance of the model and line the verts up as best you can then merge them and then tweak as needed. Theres no magic answer, just get in there and pull them about.

If you have extra faces that have been merged then delete them, that should take the crease out and again you may need to re merge.

no need for the image

cheers

Jay