The trouble with electric vehicles is that different issues can look similar. And we're working with incomplete information. It sounds to me like either the charger is unable to get to sufficient voltage to bring the battery to 100%, or the battery cannot get to 100%.
The voltage charging stops at should be pretty visible in the logs. When they reviewed them, they probably have something that tells them why the charger stopped charging. It'd be pretty clear if the charger wasn't working.
If there's a battery issue in which the impedance of certain cells increases over time, then the battery imbalance will increase and stop charging. Maybe the charger cannot charge once one cell hits its max voltage, even if other battery cells are not keeping up. There's usually a limited ability to transfer power between cells, but it's hard to do it with large currents or impedance. My RC plane's lipo batteries did the same thing when one of them started to fail.
At my work, battery capacity is based on the lowest cell's voltage. I don't know if Zero does the same, but you can see in those logs that they're adjusting the capacity of the battery based on that low cell voltage.
In short, I think they have the right idea. And they should have sufficient safety systems to prevent a bad charger from damaging the battery anyway.
Let us know how it goes.