I'm not a modder here, but any time you encounter a small ship (like a bomber or fighter) with fighter escort, you must manually fight the battle. This was a bug in the original xenophobia mod and I suppose hasn't been solved yet. As for not selling your spoils of war, I don't believe there's a reason to keep them anymore. From what I can tell, this version on xenophobia removes the ability to restore these weapons for your soldiers to use, making them only valuable as items to sell.
Also, I have a general question: What difficulty do you guys play on? Shameful to say but I've generally had to play on easy so the invasion wouldn't progress as much, but I'd still lose men almost every battle. Now since installing this new version of xenophobia I haven't lost a man and I'm 16 battles in. Does this new update seem easier to you guys, or is it just me? I generally like a challenge when I play games, and I know that the invasion ramps up fairly quickly regardless, but I've been getting misses and resists from enemy forces when they shoot me without armor point blank, and that's just not right to me.