It’s not a PDF issue so far. It only happens in ebooks. Links, nearly all chapter headings, are HTML. They render fine in all apps and in all Marginnote color modes except night mode. The reason has to do with the color your programmers chose to render links in.
As you can see below, the heading is rendered in the same blue color in all modes. This works fine in the first three modes, but you can see for yourself how it appears in dark mode. I suggest changing to the lighter blue example I showed above when rendering in night mode.