Presumably that would have come out during the investigation, not just people coming forward with their story, but verifying with hospitalized people who had a shake there, which I'm assuming didn't happen since it wasn't a part of the follow up. Shake Shack's statement also mentions it might have been cleaning product left in the machine (again, no mention of others getting sick), meaning that an employee putting it in later was ruled out, and it was thought to have accidentally mixed in. Also, the cops instantly asserted that this was intentionally targeted, and maybe it was because they are the only people who got sick, but it makes it harder to believe if it was thought to be cleaning product in the machine.
That all sounds fishy to me. And if Shake Shack and their employees aren't getting in trouble, I could see them be willing to go with the narrative, rather than go up against the NYPD and the police union for years in court since the cops are being potentially shielded from accountability from the top.
The police's story went from "We were intentionally poisoned by employees! Stay alert!" to "The investigation determined the poisoning was accidental! No harm, no foul." So that immediately makes me skeptical.