2 things firstly pop to my mind,

Check your surface normals

and

Make sure they can be attached successfully.

By that last thing I mean if one surface has only a certain number of spans etc, and the other has more or less, there could be issues like you are having.

Mike has a great tutorial regarding attaching/stitching sufaces like this in the VIP section called "Arm Stitching", so you might wanna check it out

Otherwise, a text version is at his site as well.

I believe his tutorial site is in our tutorial links database page, so check there first