They are supposed to count all the ballots. The militry vote got messed up in Gore-Bush, I remember one issue was that in Florida they decided that all absentee ballots had to have a valid postmark, which eliminated thousands of military ballots.
I’m not sure of the details but I think several states have military absentee ballot issue every election.
Do a quick google search and you will see there are a lot of issues, not just Gore-Bush. They usually are NOT counted or delayed so as not to get here in time.