Polly drank a lot of the "cure all" from the bottle causing a burning reaction to her feet and making her run without being able to stop. Therefore, she runs out of the Pizza Cats emporium and doesn't return. But later when Guido and Speedy jump into their ovens to change into uniform for battle against the bomb people, Polly is also shown jumping into her oven. Then later Polly is shown still running like crazy. There's no way Polly could have returned to HQ in her condition. Also, Polly has been shown after Guido and Speedy are in uniform when the camera pans over as usual (except on Amazon Prime where that part has been corrected but Polly still is shown jumping into her oven).