I doubt the CSD noticed you boarding, so when you disembarked he wouldn't have known that all the CE pax were seated and the ET bins full when you loaded you case.
I'm mildly surprised that the CE bins were only 40% full, they're often much fuller than that earlier in the boarding process from others doing exactly the same.
Perhaps there had been some contention over baggage on the way out and the CSD was having a bad day, I'd just forget about it.