She's using her box to pee, just not to poop? Is it every time or sometimes? My cat occasionally poops out of her box, and I could swear sometimes that it's because she's mad at me. But it's not. It's that whatever situation is making me feel that she's mad at me is not making her mad, but it's making her upset and stressing her. And that can lead to medical issues.
In addition to what BotanyBlack has mentioned, she may be constipated or have colitis, which would make her associate pain while pooping with the litterbox. My cat has suffered from both. Have you noticed that she's straining, or taking a long time in the box, maybe doing more scratching in the box than usual?