Paper ballots definitely have security problems too, it's just harder to compromise an election with many polling locations if it uses paper.

E.g., a counter can put a bit of pencil lead under a fingernail and mark overvotes on ballots they don't like, thus causing them to be adjudicated or not counted.

Those problems can also be solved with a better organised electoral commission. Here in Australia we sometimes have long lines at polling stations, but I’ve never heard of any of those other issues occurring.