I just started playing and I encountered several glitches in the first mission. I gave all my wingmen the prometheus guns instead of the default loadout. So when we attacked the freighter carrying the agent we ended up destroying the box but still disabling the freighter. I got primary objective failed notice but the mission continued on without command noticing. So I continued on and shot down the fighters. The mission didn't fail or anythign and the freighter was knocked into subspace. Eventually there was no return to base notice so I just Alt-J'ed anyway.
The mission results screen acted as if I succeeded and underneath it it told me I failed. Despite this I was still able to continue to the next mission.
In addition when I alt-tabbed later the game gave me a flickering bluescreen and then crashed and restarted my laptop.