Acquiring a mutex while pinned can cause deadlock because pinning prevents a stop-the-world. For example, the following sequence could result in a deadlock:
M1: Acquires mutex l.
M2: Pins the M.
M2: Attempts to acquire mutex l.
M3: Initiates stop-the-world
M3: Stops M1
M3: Attempts to stop M2, but can't because M2 is pinned.
At this point, M1 can't make progress to release mutex l because M3 stopped it, which means M2 won't be able to finish acquiring the mutex (so it will never release the pin), which means M3 won't be able to finish stopping the world (so it will never start M1 back up).