She was indeed contaminated with Jenova, as she herself states. She carried a child in her womb that was a combination of the genes of Hojo, herself, and Jenova. We don't know exactly how Hojo and Lucrecia made Sephiroth, but we can assume that if she didn't acquire this Jenova material during the course of the experiment (e.g., injecting Jenova cells directly into her ovaries), then she acquired it during the course of her pregnancy.
"During pregnancy, cells from the fetus cross the placenta and enter the mother's body, where they can become part of her tissues. This cellular invasion means that mothers carry unique genetic material from their children’s bodies, creating what biologists call a microchimera."
Smithsonian Magazine