This misunderstanding is apparently due to nothing more than the name of the argument: this is the "problem of evil," not the "problem of every single type of bad thing." Except of course that it really is the latter. The question is not how a perfect God can allow human beings to do bad things, but how such a God can allow any bad things whatsoever.
The most common objection to the free will defense is in fact that it fails to account for undesirable things not caused by humans. That God gave us free will may explain wars and crime, but it does not explain cancer or volcanoes. Or at least not directly: some theists believe that they are due to the Fall and thus indirectly caused by human freedom, or that Satan is responsible, or both.
But even if we suppose that all bad things are directly or indirectly the result of the choices of free creatures there is a more fundamental objection to the free will defense: no sane person holds that the freedom to act is so valuable in itself that it justifies any action whatsoever. If we did, we wouldn't put criminals behind bars. The free will defense therefore cannot account for why God is justified in allowing criminals to succeed, or dictators to slaughter millions, or Satan to send tsunamis and plagues our way. If we believe that such things are bad, then we should also believe that God, if he exists, ought to prevent them. It's as simple as that.