I use iTerm2 hotkey window feature, to pop iTerm console on top of the screen (similar to TotalTerminal or Quake console), and if iTerm2 hotkey window is active and I press "Opt+Space" Alfred Window shows up and immediately disappear, so I'm typing command to nowhere. If iTerm2 hotkey window is not active, than Alfred shows up as it should, without disappearing.
Alfred 3.0 (Build 652)
OS X 10.11.5
iTerm2 2.9.20160206