I think that in that case, it is more likely that this was a separate ballot, either absentee or provisional.
Provisional ballots are cast when they can't verify that you are a valid voter. Not sure what the rules are in Pennsylvania, so this may not apply in that specific case. By their nature, it is possible for provisional ballots to not be accepted and not count. A recount can revisit the decision to count or not count a provisional ballot.
People who can't be at the polling place on election day can request absentee ballots, which may have an earlier deadline. Absentee ballots are generally sent by mail. So you can check to see if they received the ballot. Presumably it is counted in that circumstance, and the recount should check again that it counted.
You can in general check to see if you are marked as voting in an election. The presumption being that if you are marked as voting, your vote counted. Unless your ballot was in some way unique, you won't be able to prove it one way or the other.
By unique, I mean that the combination of candidates could be unique. There were five candidates for president/vice-president in Pennsylvania, at least two for Senate, Attorney General, Auditor General, and Treasurer, probably two for Representative, often two for state representative, possibly two for state senate, and two choices on a referendum. That's over a thousand unique ballot possibilities, and many precincts don't have that many voters.
Of course, certain combinations are going to be more popular. For example, the two straight party tickets will often be the most common single choices. Picking a Constitution Party, Libertarian, or Green Party candidate would make your ballot stand out.
You might also have trouble viewing the actual ballot choices for individual ballots. I haven't tried it, so I'm not sure how difficult it is.