One problem related to noises during shifting has been reported for the 2007 Mini Cooper S. The most recently reported issues are listed below.
2007 Mini Cooper S - manual transmission would not allow gearshifts and could only be driven in first gear. Dealership stated clutch came apart after 8 months of ownership. Dealership replaced with remanufactured clutch, flywheel, gearbox oil and clip under warranty. In July of 2009 I noticed that the transmission was shifting rough and the clutch was making a squeaking sound when applied. Dealership got a work order from Mini USA to remove the clutch/transmission. On August 12, 2009 the dealership removed the clutch/transmission and replaced the plastic part causing the noise, but noticed the flywheel had heat damage and cracking again. This time the dealership and Mini USA state that this was caused by "wear and tear" and not covered under the manufactures warranty despite being covered 15k miles earlier. Current miles on vehicle are 31k with 19k remaining on manufacturers warranty.