It's an Ivy League question, from what I've read. Just because you have NCAA eligibility doesn't mean you can play for an Ivy team - we see this a lot in basketball, where guys who redshirted at some point end up transferring to another school where you can be a grad student and play your 5th year of basketball. What tends to happen in football, however, is that a lot of the players don't take spring classes for at least one semester, so from a school perspective, in their "5th year" they are seniors in college and have not graduated yet. So if he was listed as a junior this year, the question is if that's an athletic junior or an academic junior - i.e., did he take a year off academically so that he still has a year of classes left? If not, even if he has a year of eligibility left, he likely would not be able to play, at least not for Harvard.
Sorry if this isn't the issue at all - I'm taking my best guess as to what the possible holdup might be.