Unfortunately I think this is just an issue with El Capitan. I have a very similar issue where I have a badge that says I have a missed call and I have cleared my calls, reset FaceTime, and tried many other things and it still says I have missed notifications.
It's weird, I've had this issue for a while now too. Sometimes, killing dock does the trick but after the recent update, 10.11.1, doesn't work anymore, this sucks!
It's weird, I've had this issue for a while now too. Sometimes, killing dock does the trick but after the recent update, 10.11.1, doesn't work anymore, this sucks!