They should recount the paper ballots just as a check on the electronic tallies, if it’s the first time the electronic system has been used and there are such anomalous results. Especially if the exit polling contradicts the electronic results as well. Heck, they should be able to just count the number of voter signatures in the vote books and see if they match up to the number of votes in the electronic tally.
I like your thinking and agree 100%.