This is a known issue.
About 3 weeks ago, the Devs removed the AI players from the MP mode, as the diplomacy with them was causing game crashes. Also, they removed the other MP modes, such as Sandbox,
My friend and I have a MP session once a week, and have had constant MP issues. In our last MP session on Monday, with V 0.99, we played 3.5 hours in a row without a single issue.
I am hoping that the Devs will soon add Sandbox mode back to the game, so human players will be able to play each other, to win on points, without being automatically at war. Then they could add AI player capability back to the MP game.