General Discussion

1. Not illegal, but unusual. The purpose of having paper ballots is to be able to do a manual recount if the race is very close, or if there are anomalies in the tabulated numbers. The laws regarding who may request a recount under what circumstances will vary by state. Based on my understanding of the OP, there is a circumstance here where common sense would suggest that a recount of a few districts would be a wise precaution. ("Precaution" assumes that one is dedicated to uncovering fraud - or program glitches however they came to be - from any source.)

2. Probably not physically. The interesting question is this: if the tabulator recorded a vote that was not cast on paper, how was that done? Note that I work in information technology, so I could pose several theories about this. One might be double-counting of a particular ballot line for the hacker's preferred candidate. (Not that I would know how to do it, but black hat hackers can be very, very crafty.)

If the vote was cast on paper, a hand recount of the paper ballots would match the tabulator. The only fraud option I can think of that would yield the paper ballot, is there would be a very organized effort for fraudsters to cast votes for people who wouldn't show up in person. Note that this is a very difficult thing to achieve in a well-managed election. That is why there are actually VERY few cases of people perpetrating this kind of fraud. It wouldn't result in the kinds of numbers we are seeing.