While the delays in posting tolls are indicative of a problem, one mistaken billing is anecdotal evidence, not a pattern. It shouldn't happen but it does.
In the 15 or so years I've had EZ-Pass, I am only aware of two mistaken billings:
1) Illinois (home system) showed a transponder read and then a second later, a video toll (posted from a license plate scan from the violation system)
2) Indiana charged me as a five-axle truck. There's a story in there. Indiana had (don't know if they still do - haven't been on the road in four or five years) gates on the EZ-Pass lanes. Better to delay dozens of motorists than let one vehicle through which didn't scan. So if one didn't, that lane came to a standstill until an employee came out to deal with it. At the mainline plazas, they also had EZ-Pass lanes on both sides of the cash lanes (which did not have EZ-Pass scanners) with the left being designated for cars and the right for trucks. I assumed they marked them like that to separate faster and slower vehicles but perhaps not. So one day, I was approaching the "pay" (as opposed to "get ticket") plaza and I saw a long line at the one car EZ-Pass lane on the left that was not moving so I went to the "truck" EZ-Pass lane on the right. And then about two hours later, got an unexpected alert that my EZ-Pass account had replenished. And checking my account, found I had been charged about $40 for a ~$5 toll. That took a month to straighten out. For all the teething pains NYSTA is having, it does not appear to be as bad as what Indiana did which was clearly for their benefit, not the motorists (such as apparently all cars with EZ-Pass must use only one plaza lane which could be shut down at any moment to deal with a problem and then you just have to wait - so much for EZ-Pass being faster than cash).