In this node at least, goons generate colors they do not use. I have two empiricista generating 2 blacks each turn for Doom to use when they normally use green, purple and BLUE. They do not generate blue. I think this is quite unfair of the game.
https://forums.505go.com/discussion/19409
Goons can generate AP they don’t have powers for and that they don’t use. Sinpers generate Green and their green power costs 0. All ISO Mutants generate black and only 2 of them have black powers, which also cost zero. Empiricist generate black they don’t use, which is the problem you mentioned in Metal on Metal. They actually do generate blue also. They generate 
.
Holy crap, no wonder why Mystique is ridiculous with them as the only character in 
with three active abilities.