First, you have to look at how the APR is computed:

Measurement

Teams that fail to achieve an APR score of 925 - equivalent to a 50% graduation rate - may be penalized. 

http://en.m.wikipedia.org/wiki/Academic_Progress_Rate#section_3

I saw somewhere that BYU has a football APR of 928. Does anyone really believe we have only a 50% graduation rate? No. What else is going on with BYU's football APR? I think it could have something to do with player turnover surrounding missions, which I'll discuss below.

A perfect score is 1000. The scores are calculated as follows:

Each student-athlete receiving athletically related financial aid earns one retention point for staying in school and one eligibility point for being academically eligible. A teams total points are divided by the points possible and then multiplied by one thousand to equal the teams Academic Progress Rate score. Example: A Division I Football Bowl Subdivision team awards the full complement of 85 grants-in-aid. If 80 student-athletes remain in school and academically eligible, three remain in school but are academically ineligible and two drop out academically ineligible, the team earns 163 of 170 possible points for that term. Divide 163 by 170 and multiply by 1,000 to determine that the teams Academic Progress Rate for that term is 959.[8]

All of us probably know someone who came to BYU as a freshman, struggled academically, left on a mission at the appointed time, only to be academically ineligible for readmission upon his return.

The way APR is computed (see above), it seems to me this only has to happen to seven kids in the entire football program in any given year and we end up with a 929 APR (in the danger zone). 

The NCAA calculates the rate as a rolling, four-year figure that takes into account all the points student-athletes could earn for remaining in school and academically eligible during that period...

Potential Misinterpretations

While the numbers represented in the APR have a certain significance, there can be misrepresentations for people unfamiliar with what the APR is showing. For example, the APR only applies to students that receive athletic financial aid, which is by no means all varsity athletes at a university.[20] NCAA's 1,265 member colleges and universities report that they have more than 355,000 student-athletes playing each year. Approximately 36% of these NCAA student-athletes receive a share of the $1 billion earmarked for athletic scholarships.[21] Another common misuse of the data occurs when APR results are compared between universities. This is usually not a valid comparison unless it is viewed alongside the graduation rates for non athletes at the institution. For example, one institution may have an APR representing that only 50% of athletes are on track to graduate which seems like athletes are under performing at the university. 

Like BYU.

However, if the graduation rate for non-athletes is also 50% then the low graduation rate for the athletes is not a student-athlete problem, but a university wide problem.[22]

Ding ding ding. I am a huge fan of missions. I think we should keep at them. However, for purposes of our APR, throwing a two-year sabbatical in the middle of a four-year bachelor degree program is not a recipe for success. I would expect BYU's athlete APR is not much worse than the APR of the general student body. Missions are a wonderful thing, but they throw a huge wrench in the works for NCAA compliance.

Furthermore, it is not always relevant to compare APR scores across universities because the academic rigors between universities differ.

I can't remember where I read it, but if memory serves, BYU has more stringent academic entrance requirements than either 1/2 or 2/3 of P12 schools and almost all of B12 schools. Several years ago, JohnHaddow posted here that BYU's average ACT was 7 points higher than Utah's and GPA was eight tenths of a point higher than Utah's. 

So when our athletes struggle with BYU's academic standards, comparing our APR to lower-end academic programs isn't quite fair:

For example, at some high performing academic universities freshman struggle with eligibility because the workload is hard to deal with initially, but in the end, those students find academic success.[18]

This is the point, really. BYU is a high performing academic university. If our freshman student athletes struggle (as many do even at average academic institutions), and if those struggling freshmen leave on missions and are not qualified to return, our APR is screwed. Those struggling students don't have a chance to find academic success in the end. If it happens to more than 7 kids, we are really screwed. 

If you think about it, it is amazing we have not had more APR problems. BYU is a school with rigorous entrance requirements where many of the athletes in men's programs have a built-in two-year hiatus. There is a chance that a kid who struggled academically as a freshman will be denied reentry after that hiatus. 

Of course, I have made some assumptions to reach my conclusions here. I would love to be shown that my assumptions in this post are all wrong. I would love to learn that the fact our football squad struggles with a near 50% dropout equivalency rate is a blip that can somehow be attributed to the Gary Crowton era.

The missionary program is one of the most wonderful things about the Church. It is an inspired program that changes the lives of those who serve and those whom they serve. I simply point this out to explain the unique challenges at BYU with NCAA compliance. This is particularly true for the football team, which has like ten times as many scholarship athletes to keep track of as the basketball team.

Given the football team's APR struggles, the success Dave Rose has had with the basketball team is even more remarkable.