When you connect a command block to a comparator clock the command block can't keep up with the comparator clock.
To Reproduce:
Place a comparator and behind it place a Redstone block. Set the comparator to subtract mode and use Redstone wires to connect the front to the side and then connect it to a command block.
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Make sure the redstone you connect the command block to is actually toggling. It might be going between power levels 1 and 15, which is normal activity. Try dragging the redstone a couple blocks away from the clock.