I have not had any problems either with the quilting. If I have a lot of seams on the outside edge of the pieced top, then I do a basting stitch before I quilt. If the quilt has single fabric borders then I don't bother. I usually cut my last border about an inch larger so as to have trimming/squaring room. I do start and finish off into that trim area. I, also, sew my bindings on with the machine and that creates another double seam across that trimmed area.
The one time I had problems with my quilting was when I didn't quilt enough in the center of the quilt. I had quilted at the 4 inch minimum that the batting required, but the weight of the quilt when I moved it, popped seams in both the blocks and in the quilting itself. I reloaded it on the long arm and took care of that.