for the merge did you use mirror option or did you pass them one by one? sometimes maya's merge doesn't work very well, I would advise you to check the edgeloop again. If you worked on the geometry before reattaching it, you might also have an extra vertex in those points
it happens sometimes and i never figured out why exactly, but the quickest solution for me is to delete those faces and then refill it. The cleanup tool doesn't always catch whatever the issue is. also may want to check out the symmetrize tool if you aren't familiar, think its covered…