This was resolved after about 2 hours on the phone with the company who manages the machines, but I still don't use them anymore.
How can you prove if it was you or them that miscounted?
Modern “envelope-less” machines do not have this risk.
Counting cash by hand is surprisingly error prone. I ran a snack bar in high school and I would hand-count a large pile of grubby $1s before bringing to the bank. About once a week the total from their counting machine would not match my tally. I think even once it was the machine that got it wrong.
If you’re face to face with a human you can error correct before the pile of cash disappears.
See https://krebsonsecurity.com for a ton of articles about various skimmers and scanners that have appeared in ATMs and gas pumps.