Yep, happening to mine as well, but not even WhatsApp is showing up - I did change it to light mode and looks like the notification dots are all white on black background and I guess they didn't think that in dark mode it would have to be BLACK on white background...
But seeing as it's not affecting everyone maybe it is also to do with the app icon theme we're using? So I'm going to have a play to find out if I can get it to work (just annoyed that I might lose my current theme as I played with it for ages to get the colours perfect...)
Do let me know if you've found a solution though!