I've been experiencing an issue through a few versions now where my system tray will sometimes be missing icons. Just a minute ago my system tray was only showing one icon next to the clock and approximately 5-8 icons in the expanded tray when opened. Obviously, an app icon I was looking for was not there.
I went into start11 config and to the taskbar section and toggled off "let start11 enhance the taskbar". That restarted explorer and then the icons were there in the default windows 11 taskbar. I toggled that back on, which restarted explorer again, and now I have my expected 4 icons in the always visible area and 11 icons in the expanded area.
Next time it happens I will just try restarting explorer, but I've noticed this happen at list 5 times over the past 3-4 months.