@lizzypooo,
Are you trying to figure out how to enforce a rule after the fact, or are you trying to figure out how to be fair in spite of the human-induced computer error?
If the former, then I think engineer's suggestion to downgrade a random 3-pointer might be the best you can do after the fact.
If the latter, then I agree with joefromchicago that the latecomers are actually at a disadvantage. First, it sounds like they've already forfeited a potential point for missing the Thursday game. Second, they've got fewer options for selecting 5 3-pointers. Under the assumption that an informed fan will do better than a random number generator, more options means a better chance of correctly picking more 3-pointers. To illustrate the point, assume they waited until there were only 5 games left for the week. They would have no choice at all, and the five remaining games might happen to be the toughest to pick a winner. And if they happened to be the easiest to pick, then it probably doesn't matter as they would likely have picked them anyway.