I’ve seen this often when opening smashwords epubs. Their guide explicitly states for users to define the text color as black (color:black). When you change to night mode, or otherwise specify a background color in the css, this prevents the device from changing the text to a complementary color.
I could see this happening with other “automated” ePub software designed primary for print. As Diap mentioned, I doubt this is a Sigil issue. Try searching your CSS file(s) for “color”.
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