Experiencing same thing with iPhone 6 Plus running iOS 9.1 and Avic-8100NEX F/W 1.03
Utilizing CarPlay via USB1 (Upper USB port).
As iPhone is muted when this happens even when unplugged from head unit USB, I'm thinking it's an Apple bug.
Upgraded this evening to iOS 9.2, Hopefully this fixes the problem.
Otherwise I'll contact Apple support, see if they have any better solution than hard resetting the iPhone each time this happens (Long press Home and Sleep button until Apple logo appears).