From what I read I get the impression that their clutch is a possible design flaw.
There is also some drag issues that might have the same root cause as this grinding noise. For example read Post in thread
While riding at Brown County State Park in Indiana this past Saturday, we stopped after a climb and chatted with another group of riders. One of them was a Trek employee involved with their ebikes (and riding an EXe) that had come down from Wisconsin. Among other questions, I asked about this drag and he confirmed it is a real thing caused by the clutch not fully disengaging. He told me the best way around it is to turn the bike off to climb with no assist. He also said that early on they just used warranty replacement to deal with some problems and that this drag is not considered a warranty item now.
'Official Trek Fuel EXe Megathread!'
Fuel EXe - Official Trek Fuel EXe Megathread!
Seems like something is going on behind the scenes.
There are also rumours about a new motor revision and that its introduction into the production is causing delays. My LBS told me first that my bike is delayed because Trek told him TQ wants to improve "something" first. And then a month later Trek told him the missing part is the motor.
For me this sound like they planned to introduce a new motor revision thats delayed. Maybe they had to swap many motors and noticed their is something wrong. And they would rather take some deliver delays then warrantying anymore motors.