You're saying that bluetooth audio for your phone calls is coming out the car speakers, but the phone is using its own microphone and not the car's? That's a weird, weird failure. Generally if one channel on a bluetooth profile is working they all will. But it's bluetooth and it breaks in strange ways I guess.
Start with rebooting the phone. Most likely this is where your problem is. If that doesn't work reboot the car MCU too (hold down both scroll wheels for 10 seconds until the display shuts off and restarts). If that doesn't work, delete the pairing in both the car and phone UI's and start from scratch. And if it still doesn't work I'm out of ideas; try a different phone to see if it's unique to this combination I guess.