I think this might be simpler than it may seem, and I think it comes down to the old lesson of building attraction and comfort. This girl, you’re meeting for the first time in person. She’s clearly attracted to you, having stepped outside her own set boundaries of meeting in public first, and coming to your house (already a decently big move for first-time meeting). She brought wine, meaning she’s clearly contributing, understanding that drinking is involved and things are more relaxed, easy-going when alcohol is involved. I don’t think she truly worried about things progressing forward.
With this though, she built herself a backup in case things went bad, with ‘I have to leave soon’. This is for if you turned out to be an *******/psycho/whatever, or just things ending up being deadpan awkward. This gives her an out that’s pre-established, so it’s not out-of-the-blue if needed later. Tied in with meeting in person for the first time (and previous push to meet in public first), this seems like a normal thing to see.
I think if I was playing it, I would take it relaxed and say ‘No problem. We can just enjoy dinner and talk a bit.’. Let her have her out, and she can relax a bit. Give her the chance to get adjusted to knowing you in-person, build that comfort and rapport. Even getting comfortable in your house and knowing it. If things went well, she’d forget all about her having to leave soon, and it’d continue forward. Worst case, you set up another date, leaving her with a good feeling to miss and wanting to re-engage.
In this case, telling her she could leave probably amped up her decision making to stay or go, not part of her original game-plan -raising stress. And she stayed (due to built-up attraction). This brought her uncertainty of not knowing if she was ready to be dating yet (stress release), trying to get reassurement from you on a baser level. Nervous as ****. But as the push from you was to go (again), she took it. Later I think she probably felt she ****ed up, or caused the interaction to tumble (but still attracted), so she tried to put it back to normal talk.
Dash Riprock has made some great comments as well.