Powering one face of a command block with a clock provides constant power, until switching.

When powering one face of a command block with a clock it has a chance to get stuck in the on position instead of pulsing. Removing the power source and connecting it to another face usually works.
Video explaining bug: https://www.youtube.com/watch?v=LneAPxUBCKo&feature=youtu.be
World Download attached to issue.