I found it very interesting in looking at the accepted entries for the Stanford invite this year as I only see one NON-NCAA 4-year school (Concordia-Oregon) represented. NOTE: They are NCAA D2 next year, currently NAIA.
Could this be because a few races, most notably the men's 5K, were won by non-NCAA athletes. Men's 5K was won by Eric Avila of Southern Oregon (NAIA) - he has subsequently gone pro and story about him can be found here on letsrun.
It's not that NAIA athletes aren't capable of running and/or have not posted marks good enough for inclusion. I am aware of a 14:10 5ker, 9:08, 9:10, 9:12 steeplechasers to name a few who were submitted as entries, yet not accepted. Conversely, I know of multiple athletes that do not even have marks within the last year that were accepted and at least one athlete that is well off some of the non-ncaa submissions (15:05 5k accepted).
I will be honest in saying Stanford has every right to accept and deny any entry that they want. It is their meet. I am perfectly fine with that. However, it is pretty obvious what has happened here with who they did and did not accept. If they are going to do that, they should just say so up front.