Weird I just ran into this same thing! Fresh install just in the last couple days.
Also a duplicate color palette listed in the theme settings, one with no default colors showing… (I did not yet add / edit any colors.)
However when I switch to the “Colors” tab only two (Light + Dark) show as expected:
I did not intentionally re-run the setup wizard but I did quit + resume partway through (had to restart after my machine froze). Not sure if that may have something to do with it…