I emailed Classic Elite and it turns out the holes are not from the short rows, but from the bind off that the pattern says to do at the beginning of two rows. After the short rows, you rejoin and knit the neck in the round. What the pattern did not say was that you have to pick up those 4 sts that were bound off and knit them with the rest of the sts. It shouldn't take too long to fix. Just need to finish some gifts first.