It looks as if Ducati are not going to offer Marc Marquez a factory seat for next season. Reading between the lines, perhaps they don't like his "no compromises" riding style, it perhaps isn't the right fit for them.
Are there any other similar instances when this has happened? I can think of riders who deserved works rides, but never really got the chance, but not really of a rider who definitely had the speed not being given a ride or having to drop down quite a bit in the pecking order of bikes to get a works ride. Well maybe Kocinski perhaps and Gobert, both were fast, both brought "baggage" with them, but neither was a championship contender at the time, good as they were. Kevin Magee was sidelined after the Bubba Shobert crash but again not really a championship contender.
Perhaps the closest I can think of, is that I have heard that Steve Baker's chances of retaining his works Yamaha 500cc ride for 1978 were harmed by a big fight between his girlfriend and sister (I think) in the paddock in front of the Yamaha bosses, who didn't think much of it. I don't know whether this is true though.