It's interesting to note many games and stories have inherent assumptions about their rules borrowed from real life(TM) yet authors and game masters fail to consider logical extensions. An example in D&D 1st to 3.x edition is the prevalence of powdered silver as a cleric spell component. It implies relative ease of access to silver by any priesthood. Not a problem in a game with a common silver standard.
There are places where this is not applicable. Settings like Dark Sun where sorceror-kings and history have depleted resources. Or Ravenloft where werebeasts aren't only prevalent but rule certain realms. Another example from D&D is diamond dust. Diamonds aren't plentiful without a source. There are other examples but you get the idea. Wool without sheep? That may be a problem...
Rather than despair at the inconsistency, it's worth thinking of this as a way to give the game or story a bit of distinction. An explanation why is needed as you will be asked by those inconvenienced by - or who wish to take advantage of - the situation. To have arrived here, a series of events have taken place. All you need to do is to establish what they were.
Those with improv genius and opportunity will riff something pithy and insightful into the human condition and the apparent inconsistency. The rest of us have to prepare something - which requires thought and a little bit of judicious problem solving. I recommend borrowing a couple of methods to facilitate this as you'll need to identify the root causes and possibly turn it into a scene or even a whole story.
The first is taught by three-year old children the world over. Ask "Why?" in response to an answer to your question. Repeat five times. Each "Why?" sparks an answer which leads to more information. More than five and whoever you're asking may try to strangle you. Asphyxiation is bad and it reduces my readership. Resist the temptation. It's been tested by children so you don't have to!
The second is Dr. Rotwang's adventure funnel which offers a goal, sets obstacles in it's way and provides details to give additional flavour. Use the inconsistency as the goal (in the first example, the presence of powdered silver despite the setting saying otherwise), set obstacles (the whys it's not working that way in the setting) and use elements of the answers to your five whys as details.
Doing this is no excuse for bad research or sloppy plotting. It does smooth rough edges off and provides opportunities for campaign branding. Done well, your audience will buy into the story when they find that the apparent inconsistency has a logical and internally consistent explanation for why things are the way they are.