It is possible that you’re knitting too tightly and this is causing the yo’s to overlap the other stitches. When you first do them, they can easily look like they’re overlapping. On the next row, though, if you make a point to work the yo stitch in it’s correct order, you can should be able to sort them out, get them lined up again and have the hole where it should be. Have you tried knitting on larger needles to loosten up the stitches a little bit?