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Ahmed Magdy Hatataleft a comment
Dark mode was working flawlessly. At some point I installed NightOwl and continued to work perfectly up until one of the latest updates of the OS to 10.14.2 or to a newer version of NightOwl. I cannot pinpoint the exact time. The issue is that now if I change to dark mode there are many native apps that do not change, e.g. finder window does not change, notes do not change, safari does not...

NightOwlEasily toggle your Macs Dark Mode with this menubar app.
