For the batteries, a defect could be introduced that overheats the mechanism. The battery is an effective productor of perpetual energy, something that by all means should be impossible to the first and second laws of thermodynamics. (But again, shifts!)

It could be either made so that the battery delivers far too much energy that it could fry the motherboard (a defect in PC's -- hence why there is a safety lock that shuts a computer down if the cooler stops working... which could be toned down from the droids, by increasing the temperature tolerance, perhaps), or ruin it just a little so it gardually loses energy in combat situations.

Even the tiniest leak of energy that forbids the battery from being a perpetual energy mechanism could have serious effects on the droids.