Hey Cell, sorry to hear you had a problem like this. If there's any more details you can give us it would help a lot in fixing the issue. For example:

-Did this happen during a mission, on the Salem, or during a loading screen?
-If it happened during a mission, did it happen after something you did or during the enemy turn?
-Do you remember what exactly was happening when the bug occurred?

Thanks!

During a mission where I see a ziggurat and enemies are teleporting in.
It happened after the enemies all went "suicide bomber" and killed someone.
I think I had just "shutdown" their portal by having destroyed the third "thingey".

Had this happen to me on the same mission, The Hand that Guides, after I destroyed all 3 of the crystal things, it said evacuate when ready, and then I wasn't able to click anything anymore. I noticed my usual grid that shows up was gone too. And I couldn't end turn or really click anything I had to ALT F4...