One problem related to manual transmission has been reported for the 2009 Mini Cooper Convertible. The most recently reported issues are listed below.
2009 Mini s. Flywheel and clutch burned up at 9000 miles. Went to dealer and had to haggle to get this covered. They made me sign out that it was possible it was my fault. I would not sign it. This issue is on many of the 2009s. What I did was to hold strong that any car at 9000 miles should never use up a flywheel/clutch and it was their issue within the model.