I also had issues. Back in my day (2007), the paperwork asked when your planned return date from your mission was. I put it two years from my MTC entry date (beginning of June). Because of the way the transfers worked out, I came home only about a day before Summer term started. BYU determined that I should have enrolled "immediately" upon my return. They made me re-apply for admission. I was able to easily get back in because it was a bit less competitive and I think they were trying to do a "make-up call".
BYU has zero flexibility on this type of thing.