Pressure plates not working properly.
Please check image:
Villager is stepping on the stone pressure plates, and signal is transmitting through the redstone dust. However, look on the other side of slime block at the torches. 3 are on, but the other 3 are off. All 6 lower torches should be off, but the 3 torches on are bugged.
The bug remains until the stone pressure plate is removed and replaced. Removing the villager does NOT make the stone pressure work properly. Only removing the pressure plate fixes the bug.