According to this NY Times article the ACLU has been shredding some documents over the repeated objections of its records manager and in conflict with its longstanding policies on the preservation and disposal of records.
It's summed up nicely early in the article:
The matter has fueled a dispute at the organization over internal operations, one of several such debates over the last couple of years, and has reignited questions over whether the A.C.L.U.'s own practices are consistent with its public positions.
The organization has generally advocated for strong policies on record retention and benefited from them, most recently obtaining and publicizing documents from the government about prisoners at Guantánamo Bay, Cuba.
Janet Linde, who oversaw the A.C.L.U.'s archives for over a decade until she resigned last month, raised concerns in e-mail messages and memorandums for over two years that officials' use of shredders in their offices made a mockery of the organization's policy to supervise document destruction and created potential legal risks.
"It has been shown in many legal cases over the years, including the Enron case, that if a company has an established and documented shredding program they will not be liable if documents at issue in a lawsuit are found to have been destroyed," Ms. Linde wrote in a 2003 memo. "If, however, the means for unauthorized shredding is present in the office we cannot say that we have made a good faith effort to monitor and document our records disposal process."