I have the same/similar issue on Android. First on a Nexus 4, which I recently replaced with a Moto X Pure 2015, and it did it as well. Does it occasionally on inbound and outbound calls - the car and the phone shows the bluetooth connection active, but the audio is going through the phone speaker. If I toggle the sound on the phone to speaker phone and back to bluetooth, then it will start working.
This started happening about 18 months ago after an Android OS update - not sure which one. Prior to that there was an issue where the call would just drop if another call came in while you were using the phone on bluetooth, but that was fixed.
I think if I disable wifi it works more reliably, but not sure on that, it might be in my head. This hasn't happened on my Motorola Roadster bluetooth in my other car, only with the LEAF.
This is all in a 2012 LEAF. I also have a 2015 LEAF, but haven't driven it much yet to know if it happens there too.