The noPassthrough/prepare_confict.js test enables the profiler on a collection, which holds a MODE_X lock on the database, in parallel with beginning an update operation in a transaction. This occasionally results in a LockTimeout error on the update command.

Enabling the profiler with the profile command  should be moved so that it completes before doUpdateTransactionPrepare starts a parallel shell. This will ensure so that no conflicting locks prevent the update command from completing.