I found that if you make a redstone comparator clock, and break the power source that powers the comparator, the comparator will sometimes stay powered, even though it shouldn't be. As shown in the screenshots, the debug menu also confirms that the comparator is powered, but any adjecent redstone isn't. A server restart (MP) / world reload (SP) / chunk reload (F3 + A) / block updates don't seem to fix the comparator. The problem only occurs when the comparator is in subtract mode.