They have, but unfortunately they get innocent people and lock them in solitary confinement for months eventually resulting in $1.6 million dollar pay outs and presidential apologies to the accused.[1]
Lee pleaded guilty to one felony count of illegal "retention" of "national defense information." In return, the government released him from jail and dropped the other 58 counts against him. Judge Parker apologized to Dr. Lee for the unfair manner in which he was treated. The judge also regretted being misled by the executive branch into ordering Dr. Lee's detention, stating that he was led astray by the Department of Justice, by its FBI, and by its United States attorney. He formally denounced the government for abuse of power in its prosecution of the case.[20][21][22] Later, President Bill Clinton remarked that he had been "troubled" by the way Dr. Lee was treated.[23][24][25][26]
Which references a CNN article that states: "Then-President Clinton issued a public apology to Lee over his treatment."
[5] http://www.cnn.com/2006/LAW/05/22/scotus.wenholee/
It would be nice to find a full quote or video of the apology to be more certain that it happened and it was not a sorry, not really sorry, apology.