One classic mistake made by cartoon supervillains concerns the complicated piece of machinery that is inevitably at the heart of their secret plan. It might be a time travel device of some sort, or a machine that strips the opposing superhero of their power, or a key part of a world domination scheme.
As a way of illustrating just how evil and ruthless they really are, supervillains will often kill the whole team of scientists who built the thing, perhaps by having them all drink poisoned champagne. This does make a certain measure of sense. Killing the scientists keeps them from going off and telling people about what they did, which could cause problems for you.
That being said, I strongly object to the timing that is frequently used for these killings. The supervillain will kill off the science team right before testing the device for the first time. As anyone who has worked on anything remotely technical and complex can tell you, this is the worst possible time to kill off all the people involved. Chances are, the machine will not work properly on the first try and that the only people who can figure out what went wrong are the people who designed and built the machine.
By all means, kill the science team once you are confident that you have a machine that will do what you want. Build it, test it, build an improved model, build a backup copy or two, and then hand out the glasses of killer champagne.