With fill-in-the-bubble ballots, a typical error would be printing the ballot with the candidates in one order but programming the scanner with the candidates in a different order. There was a famous incident of this happening [in] Pottawattamie County, [Iowa], in 2006 in its June primary. The net result was that the numbers that came up were pretty nonsensical and bore no relationship with anyone’s expectation of the outcome of the race. The election officials noticed. They did a hand count, and that completely resolved the problem. And they could because they had paper ballots.
I think like most things there are tradeoffs and the qualities most needed in the system run counter to one another--speed can cause errors to be missed, security reduces access, etc.