Figured it out! What happened was, the logic for a defensive penalty at the end of the half fired, but it didn't take into account the fact that you probably don't want to extend the half if you just scored a touchdown. It also just plain didn't apply the penalty correctly.
I'm working on a fix, but I'm not going to push it right away - I'm going to be going on vacation over the next 10 days and won't be around to fix anything if my fix for this blows up, so I want to take a little more time to test and watch before putting it into the beta version. Fortunately, it's a rare occurrence - but it's not unlikely that it will happen again.
BTW, there was another weird penalty in that game - a facemask was called on a touchdown, and the penalty put the ball at the 1-inch line. I'll be dealing with that issue with the same update.