There's a few different ways she could be interpreted.
The easiest is referring to Harry's first three cases. Storm Front went well for them but ThreeEye didn't exactly expose the cops directly to the supernatural. Fool Moon vastly less successful with the loup-garou rampage through the precinct, as you noted. The raid on Leonid Kravos before Grave Peril went well, but the aftermath included a cop wrapped in spiritual barb wire, and Murphy being directly mind-raped by the Nightmare. After that Murphy was clued in to the bigger picture in the next book, and kept the cops less involved.
She could also be referring to the events of Proven Guilty as the second bad event. Splattercon!!! was covered heavily by the cops and they could do jack squat about what happened, even with Murphy directly in on Dresden's work and other departments involved investigating and covering the show floor. That had more public consequences and innocent lives lost on Murphy's watch, so that is how I would interpret it. That would make the Fool Moon (bad loup-garou) and Grave Peril (good raid, limited consequences to select cops) the other big cases for SI, and the ThreeEye case could be just written off as business as usual.