I don’t understand you at all.
In that windows of yours there are apps that is installed in template/qube on the left side.
On the right side are apps that was moved to be accessible from menu.
Xfce Terminal is not a system, it’s an app. All those what you see over is installed apps both on the right and on the left. Period.
The one that you highlighted, some-app (strange name) for me looks like you made .desktop file, added it to menu and then deleted it so it’s missing.
This menu don’t scan automatically all available apps.
When you install/uninstall app in template, special python script is executed that on base of .desktop file of that app generates this list. If you delete .desktop file by hand from terminal/thunar then this menu/settings windows know nothing about it.
And if you have app added to menu on the right but you uninstall it from template then it will stay on the right side in settings window as missing.
You need to remove it from the right side.