I use spaces with the "Displays have separate Spaces" setting selected on OSX 10.10.
In this mode, OSX seems to have a "phantom space" that disappears when a monitor is unplugged, and reappears when it's plugged back in. I'd expect to have that space always exist so I can manage windows the way I want them.
Is there any way to stop this from happening?
Anytime I plug a display in, a new space is created. Then, when the screen is unplugged, a space is removed and combined with another, even if I've put windows on that new space and set it up the way I want it.
To me, the combined spaces are completely arbitrary. The space on the separate display gets combined with another space – often one I haven't used in ages – then when I plug the display back in I get two separate spaces again.