I don't know if this is the case here, but I have noticed that when I do yo's, I THINK when I do a k1 yo, it pulls the back of the k stitch up over the needle a little bit. When I purl back on the other side, I have to be careful to make sure that I'm knitting into the yo and the back of the k stitch rather than into the two legs of the k st that was pulled over. When I get to that point on the back of the knitting, I have to consciously kind of roll the pulled over stitch back into place in order to knit the proper stitches.
If this makes no sense at all, let me know and I'll try to post a pic. It happens alot on a shawl I'm making.