Easy. Serial numbers. Like any other anonymous system (paper money, raffle tickets etc) you assign a number to every valid ballot. Should the same number appear twice, or not appear, then you know something fishy is happening. Any extra fake ballots should be discovered, so long as the originals are not removed from the systems. Throw the numbers around randomly and creating undetectable fakes become very difficult.
You already have a log of who showed up to vote. Compare the number of shows S with the number of ballots V which must be <= S due to poorly marked/unreadable ballots. Simple.
Edit: and this all statistically correlates with exit polls. It's very, very hard to fake all three of these in order to rig an election.
https://en.wikipedia.org/wiki/Australian_Senate_special_elec...
Which is why it's important to fix this earlier rather than later.
If it's your goal to cast more FUD on the issue, that's your choice. I can't even ask to you be honest about it because that wouldn't be congruent with spreading FUD.