I cant say exactly where but I've seen that a lot when I'm designing ships in the sandbox game I'm playing now. Never that extreme but it's enough to mess things up. Usually it's like a weapon that it says takes 11 slots but after placing it I'm only 9 slots down. And if the ship only has 10 slots left it wont let me place another one of those 11/9 weapons.
I even designed a ship once that was over the max by 1 point. it wouldnt let me build it but, still, the design was there.

I had it occur last night in 1.1 but I don't yet know how to reproduce it. Just wanted to verify that it seems to persist in the lastest patch . . .

Makes for some fun ships though

I definitely started a new game after updating to 1.1. I don't know what causes it unfortunately. I don't remember doing anything particularly strange in the shipyard . . . just suddenly components I added to a particular design were talking less space than they were supposed to.

If it helps . . . I remember getting the ship full enough that an additional component wouldn't "officially" fit but there was enough space to fit it if it was resized to the size of the other (identical) components I had placed before it. The ship designer wouldn't let me place it though . . .

When I get some time later I might play with the shipyard and try to figure out how it happens.