You know, you’re trying to use Mission Control and this single app on all desktops annoys you. For me it was Firefox. Somehow I must have enabled it accidentally. So I’ve searched for a solution and even tried
osascript -e 'quit application "Dock"'
And even repairing disk permissions using Disk Utility. It didn’t work. The solution was to open context menu (Right click) on the icon in the Dock and chose Options > This Desktop to keep app on this Desktop or Options > None to have no settings.
How about you, was this annoying to you too.