I just had a game where the red empire had only one city left surrounded by my territories. I started a war against them, killed the few armies they had left and then succesfully sieged their last remaining city. Then when I went to force them to surrender, I couldn't. Turns out the yellow empire who did not participate in anyway vassalized them. I had 100% of red empires territories and someone else just vassalized them, so I consider this a bug.

You shouldn't be able to vassalize an empire when someone else currently at war with them owns 50% or more of their territories (Let alone 100%).

Had this happen to me, too. I ended up getting their cities when it happened, which I was thankfully able to accommodate, but it seems like an issue, for sure.

Yeah, I think the root cause of this is that an empire possessing no capital (no remaining cities) sets its war support to 0 at the start of the next turn, and AIs get to end the war before humans do.  AIs should have the opportunity to "Force Surrender" only after humans have taken the opportunity to do so.  Force Surrender could be done in the order of most-support to least-support, or most-war-support-damage-done to least.  Three-person wars and being able to run wars beyond their natural ending point also complicate things, but I 100% agree that the situation you're describing shouldn't happen (and has since the game came out :(    ).

This is a problem that occurs not only in war resolutions, but in most things that tend to be resolved at the start of the turn, the AI deciding everything while the players are closing the dozens of messages that crowd the screen.