One problem related to manual transmission has been reported for the 2005 Mini Cooper. The most recently reported issues are listed below. Please also check out the statistics and reliability analysis of the 2005 Mini Cooper based on all problems reported for the 2005 Cooper.
Transaxle on the Mini Cooper failed. Unit contains sealed bearings (so I'm told), that are not serviceable. Therefore, I had to buy a complete new unit at a cost of $3,000 ()included $900 labor). I understand this is not an uncommon failure for Minis, and that Mini and BMW are refusing to work with consumers to address this problem. However, they have apparently changed the design, recognizing the poor design of the original unit.