A window came up with this error message in it:

SanityCheckManageSquadType failed: ManageSquadType=0

What I think caused it:
I had just colonized a planet that I had just taken from an enemy but the battle was still raging. I built a handful of orbital hangers with the intention of using their fighters to help me finish the battle. I was queuing up their squads of fighters when the enemies ships bombed my colony off the face of the planet. That is when it happened.

After pressing "skip" on the error dialog I was able to resume playing.