The reference in the rules is right below the one for Heroes and villains, on p. 16:
Running out of Cards in the Bystander, Wound, or S.H.I.E.L.D.
Officer Stacks wrote:
If one of these stacks runs out, the game continues. If a player would gain one of these cards, and there aren’t any more of that card left in the appropriate stack, then you don’t gain that card and the game continues. Don’t take extra copies out of the KO pile.