Hey, curious to know if you're still getting this? I've noticed my Mac has been doing this since auto dark mode was first introduced. I also noticed that when using dynamic desktops with simulated sunsets (e.g. the stock Catalina dynamic wallpaper), these would also be a little bit off and would still show a sunset at around midnight, which would then cut to a sunrise later in the night/early hours of the morning. It would never *actually* show the midnight wallpaper.
After doing some digging a while ago, I found that macOS decides on the wallpaper it shows if set to dynamic depending on the position of the sun, including when it's below the horizon, and I would assume that auto dark mode works in a similar way. If you want to get technical, there are multiple levels of twilight between sunset and night, which depend on how far below the horizon the sun is:
Civil Twilight: 0º - 6º below horizon
Nautical Twilight: 6º - 12º below horizon
Astronomical Twilight: 12º - 18º below horizon
Night: beyond 18º below horizon
Because my location is north enough to not have night time during some summer months, it probably never triggers the midnight wallpaper because the sun isn't low enough past the horizon. My running theory is that the threshold for dark mode probably works in a similar way, and is set to one of the twilight zones rather than actual sunset. My dark mode turned on around an hour after sunset today, which according to this website
https://www.timeanddate.com/sun/ was when the sun was at an azimuth of -8º. Maybe this is a trigger?
Might be worth having a look and seeing if this lines up with your local -8º azimuth times? Tbh it would be pretty nice if Apple let us change this threshold if it is that...