Note that you must make sure and unpin the app from classic start before exiting. Usually restarting the app like Paint3D after I unpin the app restores the icon. I noticed that as well sometimes as I was doing different repros. This is great for Win32 apps but it appears as though this is causing problems for modern apps.
The issue I believe is that Classic Start is specifying the icon used for the process on launch.
Repro steps (assuming you have Classic Start installed, assuming you have the 'Show Apps Menu' option enabled) I noticed this on Windand 1809 build - if you pin a Windows 10/modern app like Edge to the Classic Start menu/Open Shell menu, then launch the app, then close the app, then launch the app again (sometimes you don't need to launch twice) the app will not have a taskbar icon.
