Hmm. I would suggest maybe making your wraps tighter then. (Or if this is after-the-fact, distribute the extra "puffiness" or slack around adjacent stitches with a crochet hook.)
Also, are you making sure the 'wrap' ends up on the WS? If the wrap is worked correctly and both the wrap and corresponding st end up on the WS it'll virtually disappear but if it ends up on the RS it'll cause a bump. Not sure that helps. Perhaps you could post a pic?