Wikipedia is not a great source for truth of specific facts, but in the "Government investigation" section there is the line "President Bill Clinton issued a public apology to Lee over his treatment by the federal government during the investigation.[5] "

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.