you did well to take Zoe to the vet, I did the same thing when my dog had a similar problem a while back, the lethargy had gone away after the first day really, but she'd continued to not eat much and the poops were vile.
I didn't see blood I don't think but there was mucus. And she was rotten stinky. Had zero idea of her getting into anything, it just appeared after a walk one day. Vet's likely right that it can take a while for these things to clear up.
They did an x-ray with my pooch because she pulled away when they poked at her belly, especially her bladder (this is not particularly unusual for her), and the resulting x-ray, the vet said she had a particularly "angry" belly, gassy and inflamed and a very sore butt to boot. Even though whatever had made her sick had passed, her little system hadn't recovered so well. Vet prescribed her antibiotics to my recollection, along with medi-cal gastro. She was fine and dandy in no time.