This happens whenever I plug my MacBook into a thunderbolt display. Mission Control seems to be stuck like this until I restart. Does anyone know a fix? Has anyone at least seen this before?
Mission Control has several major bugs, including this one (still). You should be able to remedy the issue without rebooting by issuing a simple Terminal command:
launch Terminal from /Applications/Utilities/ and type the following command:
The Dock and all subprocesses will restart themselves automatically, including Mission Control.