I believe it is quite possible that the organization was not a library, but a library-related service, such as an internet service provider or other vendor.
The lawsuit itself is under a seal, forbidding release of identifying information. Interestingly, neither the press release nor the redacted lawsuit filing specifically states that library records have been obtained by the FBI -- only that this member of the American Library Association was
"hereby directed to provide to the Federal Bureau of Investigation (FBI) any and all subscriber information, billing information, and access logs of any person or entity relating to the following: [redacted]"
Considering that the requested materials include subscriber and billing information, terms not generally used by individual libraries in reference to their patrons, I believe the organization involved could be library vendor. The library vendor here could be, for example: a library system; a non-profit organization offering technological and automation for libraries; or a traditional library vendor.
What difference does this make? The movement protesting the use of the Patriot Act in libraries has focused on confronting the FBI and Justice Department regarding library records from libraries. If the Justice Department has been disingenuous regarding statements that they are not interested in the library records of Americans as the ACLU is asserting, then the library community's protests need to be wider in scope. Unfortunately, due to the redacted complaint, it is impossible to know the scope of information being sought by the FBI.