I wouldn't hamper anyone on that basis. The rogue gets to differentiate himself in shared skills with expertise. With as few skills as 5e has, overlap is going to happen and I'm not going to step in for such a flimsy reason. Nobody in my game has dibs on any skills.
The point is the two players would have to deal with it.
If they refused then I as the DM would intervene and favor the one who followed the core rules and setting rules closer.