Occasionally, when opening an app, a duplicate (blurrier) icon will appear in the Plank dock, and the app's normal icon already kept in the dock will not display an indicator.
When this happens, said app's window will show a gear icon in multi-tasking view, as shown below, as well as window spread view and the alt-tab switcher as well.
I've seen exactly the same couple of issues. I can also add that sometimes applications installed from flathub (LibreOffice) can have normal plank icons with no duplicates, but at the same time they have a gear-icon in the multitasking view.
Does it show when you are running the app?
Regardless, normal behavior is to put a dot under the applet for pinned apps and add a gear or icon at the side for unpinned apps. For some reason some pinned apps will launch the gear or icon anyway. This is the same as in gnome. I don't know why but I believe it has something to do with the .desktop file.
If it is annoying you can stop them my CTRL-right click>preferences>behavior and deselect "Show Unpinned". Of course you will also lose the icons for the apps you don't have pinned as well.
