Qualified immunity covers individuals but agencies do not need to be given qualified immunity because government agencies are covered by sovereign immunity. The government only allows itself to be sued when it decides.

Suing departments is also basically impossible because the bar for a "pattern of misconduct" is ludicrously high. Connick v Thompson is a particularly infuriating case where a man who was sentenced to death by a DA that deliberately withheld blood evidence that would exonerate could not get damages because the long history of Brady violations by the DA's office were actually a series of distinct violations with teeny differences so they couldn't be considered a "pattern."