A problem I've encountered too many times on superuser.com is that some broad questions are treated as catch-all questions, and any more specific questions are marked as duplicates even if the broad question doesn't actually have any answers which address the more specific question. Although the idea is that someone can always add a new answer later which addresses the more specific case, it rarely happens and a perfectly valid question goes unanswered. How do we avoid this problem as WW.SE grows?
In my opinion it is everyone's job to try and catch these issues. On world building we try to make the question more explicit (often by helping the asker focus on what they are really looking for).
Surprisingly often this really is just changing the title question to reflect the difference. Some times a note/explanation needs to be added in the question making it obvious why the question is not a duplicate.
On Worldbuilding we also have people willing to point out (other than the asker) why a question is different, even at the same time pointing to questions that could be closely related. I can see us doing that here. The big thing is to train people to think before voting, and not just assume that if it's in the close cue it should just be closed.
On top of that, just checking closed questions to make sure that it really are duplicates
In general you should think that is not going to happen since it takes several people to successfully mark a question as a dup (Except in the case of the DUP hammer. Which I'm sure everyone will have for safety).
If it does happen that is what the mod flags are for. So if someone closed as dup in error users can bring it up in the WorkShop or flag a mod.
Mob mentality will most likely close some of these questions but at least for the foreseeable future the rate at which questions are coming in makes it easier to set trends.
I think there is nothing to do other than leave it to the community and make them aware of chat and flags.