I'm a little late with this, but you may be using the wrong type of applique film. Some are made for sewing over, and some aren't. Personally, I like the Steam-a-Seam brand. I have never quilted over appliques, but have done the buttonhole stitch around them after I have put them on with Steam-a-Seam and have never had a problem with skipped stitches or with gummy needles. Just carefully follow the directions and I don't think you will have anymore problems. Good luck!!