I've found that this behaviour coincides with Opera misbehaving when dragging tabs to another window (bug report DNAWIZ-114163)
Next time you face this "2 clicks to close the tab" issue, please also try dragging a tab to another window and see what happens: in my case I get a thumbnail that won't go away after docking the tab. The only way out is to force quit Opera (or you can move the tab thumbnail to another desktop out of the way as a temporary workaround).