SPECTRE meeting scene
In the SPECTRE meeting scene near the beginning, Number 1 accuses one of them of embezzlement. One agent clearly thinks he is going to be punished for it, but I don't see why. He knows he's not responsible, and presumably No. 1 is intelligent enough to make sure who the real thief is before he zaps him.
I guess the other agent who is actually executed thinks No. 1 made a mistake and will fry the wrong agent.
Another possibility is that the agent who was electrocuted really wasn't guilty, but was killed as a warning against disloyalty. It would definitely underscore the ruthlessness of SPECTRE.