Dont think this is a common problem from what i know of the XT's engine. Very supprised your yamaha dealer will not repair it under warrenty, i think i would have a very harsh word with them about it. But they will probably just refer you to some small print somewhere.
As for the rev counter, they are only there to tell you how hard you are reving the engine, a rev limiter is a different thing all together. My old deauville had a rev counter but no rev limiter but have been told that if you rev it past 10k rpm the crank will break under the pressure and engine will go bang (some london courier did this for the crack supposidley).
Its was maybe something to do with the engine still not being fully run in and possibliby this is the cause of the breakage.
Feel for you about this.
as said before i would have a read through the contract of the warrenty and have a harsh word with them about it. My yamaha dealer sounds very much like yours and would not even give you a few tank of petrol let allow fix something under warrenty.