I was using ask-stack which created a new pane to show the results. When I closed the tab it went away but now I’m left with an empty pane. Actually I now have two empty panes because I stupidly tried it again.
This would be a minor bug of ask-stack or atom but the big problem is those panes won’t go away. I tried dragging tabs into the them and closing the tabs but that didn’t work. They won’t even go away when restarting atom. I guess I’ll have to find something to fix in the config file.