I haven’t taken enough calls on my Mac to know if I’m seeing this or not. But I have seen (and you can read about it in other threads here) issues where Safari takes over playback controls (the keyboard keys and Now Playing widget) far more than it should. This should happen when on pages playing audio or video, but not any other time. Many of us are seeing it far more than we should. The going theory is that this is a bug in the Now Playing widget. Perhaps your calls are pausing music as best they know how, and that is working just fine from the perspective of FaceTime, except you’re simultaneously running in to the Now Playing bug, so what is really getting paused is non-existent playback in Safari? That is just a thought. I’ll report back if I see this issue myself, but honestly just haven’t been both listening to music and getting a phone call at the same time yet since High Sierra.