I had that one, including the fact that it shows 100% on scans.
It started when I logged out on a planet and logged back in. Did it happen that way for you?
((And I never got to test repairing that ship because I boosted backwards into a crater wall while trying to take off in reverse. Don't ask...))
I logged out on planets for the first dozen sessions in this expedition (thinking it would be better as a fixed position) rather than nowhere in space, with no 99% hull issue. Several of my dirtside screenshots in this thread are from right before I logged out for the night, for example.
I didn't notice exactly when it happened, but I think it was during a play session in which I landed twice and took off. Noticed in space before I logged out for the evening. Landings were OK, but I didn't think to check again if my ship had taken a ding upon coming back to get me.... and for that matter I don't recall if I dismissed my ship at all or not.
My main concern is that if I take two more phantom-dings then I'm in the range for spontaneous SRV exploding. I've dragged my Python's hull halfway across the bubble held together with bondo and bubblegum, and if there is a decay-rate in the works then I'd be getting home with my hull in the low 90's or high 80's%. I have two SRVs which isn't a lot of leeway for funky hull decay leading to bugged kerbooms.