In order to manipulate this, you would need the entire polling place staff to be in on the conspiracy, and they would need to cook up numbers and ballots that all match. All to mess with an election at a precinct with no more than ~1500 registered voters. Where those voters are likely of the same political persuasion as the poll workers themselves. High cost, low reward.
To manipulate paper votes you need to have presence in enough voting booths and influence the votes there.
With paper it might be easier to sneak in a handful of fraudulous votes, but it will be near impossible to commit fraud at a scale that influences the elections. With software it is harder to get that access (although the article shows that one mistake by a dev can make getting access a matter of one hour...), but much easier to then commit election influencing fraud.
The fact that you do not recall any fraud either means it didn't happen (let's hope for the best) or didn't get detected. The latter is obviously very scary.
There's btw more problems with online voting specifically. It's impossible to guarantee the secret of voting. This is not an issue when voting electronically in voting booths.