It's a federal government thing. Had the same thing happen to me. You're required to list all supervisors on your resume for a federal job and I think you have to consent to them being contacted but it's been a while. We aren't even talking as part of the security clearance process, I'm talking pre-offer they reach out to your current supervisor. Was a bit awkward in my case since federal hiring stretches out for months. I'd had a 20 minute phone interview like 4-5 months prior and heard nothing so I'd completely forgotten about it. I don't think she screwed me over like the op but things were a bit tense for the rest of my time there.

Federal hiring is just weird. Take everything you know about applying for a job and throw it out the window.