Not really sure if this counts as a "bug", since it's more a matter of opinion.
Something really needs to be done about making the map's progression more obvious. In its current state, I haven't even figured out where the red/yellow keycards are, resulting in aimlessly wandering around the base looking for things I've missed.
I think that part of the problem is the extreme non-linearity to the base. I have no sense of where I'm going or what I'm doing. I had fewer problems the first time I played Hexen's first hub.
AFAIK there has been talk of an objective system, but I can't see how that could help without breaking the immersion which Torm seems so determined to maintain.