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I put down a towel under the litterbox, it's a big one and mainly to catch most of the litter she flings outside, and i've seen her poop on that before. So I'm not entirely sure. I haven't noticed anything that would have caused her to get fearful using the litterbox. I'll try to monitor her to see from now on, but it's hard to gauge when she goes poop.
Will she use paper if you put it down in the spot she uses to poop? I previously had a female cat that wouldn't poop in her tray after she had a UTI and the bad experience meant she would only go in for the pee she found painful after that. It only takes one scary or painful experience to throw a cat sometimes. I always figured I was lucky my cat used the tray for her pee as that would have been way harder to contain and clean up. With Isabelle being so young I am confident you will manage to figure out what it is that's confusing her or putting her off using the tray other than for pee.