Those are the Enslaved doing that to you. They guard every artifact*. They’re also part of the Imperial Guard storyline, which might be the part Peter was calling “bullshit”. It’s certainly not, uh, entirely fair. Suffice to say it brought me game to a screeching halt. :)
That invasion was pretty easy to deal with. I had a few vehicles who were mid-way to reinforcing my army and they were the mobile counter to the problem. The final step in the scenario is a bit more gob-stopping. Let’s just say that I don’t like timers on my missions.
As for tips for Guardsmen, I found their engineers to be invaluable. Their ability to heal 8hp of a vehicle per turn allows you to rotate whatever is being focus-fired on with a freshly repaired vehicle each turn. I pushed pretty hard and early against one AI and farmed it pretty hard, making sure that most of my units levelled up quickly. The long range artillery is also very, very handy.