My last couple of cars did it too, including the past model and the current civic.
I have thought about it and have come up with a theory. I think it is intentional that the glass fits in so tight when closed (tight enough to deform the door slightly) to make the side window stronger, for security. Imagine 2 windows, one loose fitting with some play, and one rock solid, under a bit of tension. Try to break them. Which would be harder to break? The solid one would be.