Tony and co have:
-Violated bioethics by cloning Thor
-Nearly started a war by unleashing the Green Goblin
-Manipulated the populace in a negative way
-Thrown people in prison without a trial
-Profitted from a war they helped set-up
-Enslaved and unleashed murderous super-villains
-Arguable responsible for the death of Bill Foster either as negilgant homicide or manslaughter
-Destroyed Planet Skaara (I'm still not clear if this was an accident or if they actually left a bomb to try and kill the hulk if he ever tried to leave)
-Covered-up the death of a student and perhaps set the whole thing up to acquire some technology
-Allowed a mentally unstable power house into stressful situations and recruited a known sociopath on the same team
-Stole the Terrigan Mists from the Inhumans and refused to return it possible starting another war
-Plotting the overthrow of forgein governments that oppose the current U. S. Policy
Did I miss anything?
P. S. I know all of this isn't Tony Stark, only about half of it. That is why I said Tony and Co. however he is the primary leader and has his hand in just about everything some way or another.
First thing that comes to mind...
"- You mentioned rape twice.
- I like rape."
No rapists here.