One problem related to manual transmission has been reported for the 2001 Honda Prelude. The most recently reported issues are listed below. Please also check out the statistics and reliability analysis of the 2001 Honda Prelude based on all problems reported for the 2001 Prelude.
Transmission broke. Something flew out of transmission, and shot out below cause: clutch and flywheel came apart. This was all stock, if it had shot up I might have been injured.