I think I have the same issue. At least, I'm seeing notifications that didn't play an alert when they came in and it's likely they came in while I was on a Facetime call. I'll keep checking and if that's definitely what's happening I'll log a feedback. Have you logged one?It's not even spotty. They flat out don't work at all if I'm on a call. It's as if there's some sort of "Do Not Disturb" option that's on when you're on a phone call.