This is an obnoxious but inevitable issue with a-line skirts.
For modest a-lines, I straighten the side in the hem area to avoid the whole issue. Or I will serge the bottom edge and hand-stitch the hem, as to ease the extra.
With extreme a-lines, mirror the angle at the hem line, so that the circumference at the stitching points will be the same.
Or you can use hem lace (
http://www.simplicity.com/c-201-hem.aspx). Stitch one edge of the hem lace to the folded-up part of the hem and the other edge to the underside of the skirt. The lace takes up and hides the extra, while giving a cute little inner detail. Note that you’ll want to line a skirt intended for tights or nylons, as I find the lace wants to stick.