I was having this issue too, until I finally stumbled onto a fix that worked for me. The obvious advice usually given in threads like this is "turn off 'Allow Calls on Other Devices.'" Well, on my iPhone, that setting was already off. So I decided I would try switching it on and then back off again.
When I switched it on, an "Allow Calls On" section was revealed, containing slide buttons for the other devices logged in to my Apple ID (iPads, Macs). They were all in the "on" position. I turned them all off, and then turned "Allow Calls on Other Devices" back off. Thus far, calls to/from my iPhone have stopped appearing in the FaceTime Audio call logs on my other devices.
This is clearly a bug in iOS 10. If the main slide button is off, the positions of the other buttons (which are then hidden) should be irrelevant.