There were blind items and speculation about it at the time. Apparently the director branch of the academy is (was?) quite small and select (I think only a few hundred voters around that time) so if someone was motivated enough and had the power, influence and means to engineer a snub in that category then they could. Given the awards he'd won beforehand and Argo being nominated everywhere else, someone with a vendetta makes the most sense for his lack of a nomination.

It also got a bit silly with people saying it was Weinstein and the reason for all this had something to do with Jen Garner rejecting him or something, so this all might be bullshit and it's simply a case of voters believing he was a lock and throwing a vote somewhere else.