Any reason not to leave unused breaker in the panel?
National Electrical Code simply states that all openings must be closed.  An unused breaker or cover likely both meet that requirement, so either should be fine.
I don't think there's a rule that says &quot;Thou shalt not leave unused breakers in thine panel.&quot;. But I could be mistaken.
Remove and discard the bad breaker.

National Electrical Code 2014
Chapter 4 Equipment for General Use
Article 408 Switchboards, Switchgear, and Panelboards
408.7 Unused Openings. Unused openings for circuit
breakers and switches shall be closed using identified closures,
or other approved means that provide protection substantially
equivalent to the wall of the enclosure.

It's possible that the AHJ could argue that a breaker does not meet this requirement, but that would be completely dependent on the opinion of the individual.