A hand recount of the physical ballots would hopefully expose the correct count if a modified scan-tron was miscounting.
When margins are close, you could count them all by hand.
Pretty sure we could develop ballots that are easy for both humans and scanners to read. By using computer vision rather than whatever they had in the 1980s I'm pretty sure we could find a solution here.
Even so, given the value of our democracy, I'd happily support returning to counting all ballots by hand every election.