Here's a report that shows that from 2001-2008, the FBI has had 800 serious violations of civil liberties, breaking the constitution, misusing their powers, using improper evidence and testimony in court, searching without warrants, et cetera.
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Amazingly enough, the FBI is quite good at taking care of their dirty laundry themselves. One of their main tenets dates back to the J. Edgar Hoover days, "Don't embarrass the Bureau."