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2006 Mini Cooper manual transmission

I have 26,000 miles on my 2006 Mini convertible. It started making noise while in gear. Took in to my mechanic and he says there is metal in the transmission fluid and that the metal around the ball bearings has failed and that, if he can’t repair it, I’ll need a new transmission for about 6500.00 Is this a common problem and do I have any recourse with Mini? I am the original owner of the car, but, of course, it’s no longer in warranty.

It’s true that your manual transmission’s clutch, pressure plate, etc., are not covered by your warranty, but your warranty is not expired. Your warranty covers the powertrain for 50,000 miles or 4 years.
The clutch and it’s associated parts are wear items that are not covered. That doesn’t mean your manual transmission is not covered. If the manual transmission itself - the self-contained assembly of gears and whatever - is part of the powertrain. I think the older and wiser people on this site will weigh in that issue. But the bottom line is whether or not you can expect to get Mini or more importantly, it’s parent BMW, to own up to what seems to be a very serious quality or engineering issue regarding your car’s manual transmission. A quick search found a lot of anecdotal evidence that your problem is not unique, and in fact that there are some legal options being pursued.

In your case, however, if the clutch and pressure plate and throwout bearing all are fine but there are metal shavings in the transmission fluid, the problem is with the transmission. That is part of the powertrain, and there is no way your driving habits could cause this part to fail before you either destroyed the clutch or the engine.
Read the fine print on your warranty. Have a lawyer read it. I think you might be covered after all. If not, make sure you add to the bad press.

For what it’s worth, you apparently are not alone with this problem. Without providing a lot of exact problem solving, this link to Mini Cooper forum indicates that the problem is at least not as rare as it should be.
Even if you undershifted terribly and kept your hand on the gear-shift every second of every trip, you might have affected the clutch, not the transmission itself.
I can think of no bad habit that will kill a manual transmission before that habit will first destroy the clutch or the engine. Save maybe pouring sand down into the fill tube.

If your mechanic can’t handle it he can send it out to a specialist, or you can get a trans from an auto recycling center (junkyard).