Have not been able to pinpoint the exact cause but i have noticed it a few times on hitting disconnect, have noticed it happen in the hangar and tracking station as well.
The game is still running but nothing is "clickable" pressing esc to exit the game has worked a few times but cannot click to exit. Game must be force closed and restarted to fix issue. Below is a video of what it looks like when it happened.

https://www.youtube.com/watch?v=V_EDaEOqdec&feature=youtu.be

Mods: MechJeb, DMP
Server: KerbalSpace.Spazer.net:3421

http://pastebin.com/iyGf3ZNi
occured at 18:04