I'm wondering if it's not a "closed" loft surface.
Can't figure it out with this view.

If it's the case, well, prefer closed curves to get full control OR uncheck "closed" loft surfaces option, plus the advises from Matt, you shouldn't have this type of problem.
Then simple face extrudes on the nurbsTransformedToPoly mesh.

Can't think about smthg else either.

Regards, Py.