Though The New York Times details multiple failures in its write-up, the investigation was called for based on documents from assistant federal security director Andrew Rhoades, who claims he was reassigned as a direct result of reporting security flaws within the agency. For instance, Rhoades reported that bags were missing security tags, making it difficult to know which bags had been screened. Good thing we're paying those guys!
In response to the allegations, the TSA provided a statement saying, "TSA takes any allegations of improper conduct seriously and is committed to transparency and accountability." Great. Thanks, TSA. It'd be awful weird if you said you took them as a joke and didn't plan to be held accountable.
It's sad, because if you can't trust the TSA, who can you trust? Just kidding. No one's ever trusted the TSA, anyway.