This has happened to me recently, on In Shock, on the 09 patch. 5th Council enemies were dealing 173 damage in one Strike, and took about 6-7 80 damage Strikes to kill. The Beholder, Beholder Tentacles, and Kuzmann also had far higher health than normal. We had 35 seconds to pull the levers to save Shae, during the electrocution segments. Almost managed to win it, but we still lost even though the Antagonist was friendly.
My MMR was 70 at the time, with most of my friends probably being around the 60-70 range as well. The Antagonist had 52 MMR, and was level 102. He was out-leveled by all the other Raiders, the lowest of whom was 130.
I was hoping that this would have been fixed with the 09 patch, since it seemed that the MMR of the Raiders and the Antagonist had to be within around 5-10% of each other, which would have prevented the AI from being overly weak or overly strong.
I've done a little testing with friends during this patch, and when I invaded them at 75 MMR, the AI were fairly weak. The enemies were doing about 25 melee damage with a Strike. In terms of health, Hades soldiers went down in two Strikes, 5th Council and Wardog soldiers went down in one. Wardog and 5th Council Snipers went down in one Strike, Hades Snipers in two. Wardog Captains went down in two Strikes, Hades Captains in three. Wardog Brutes went down in two Strikes, Hades Brutes in about four or five. Raiders generally had longer timers to hit switches and the like, and bosses and objectives had less health. I think they had about 75-80 seconds to hit the levers to save Shae on In Shock, when I invaded them.
The average MMR of the Raiders was about 65.
I did try to have a low MMR friend invade us, but we couldn't find each other on matchmaking. He had about 40 MMR, and I had about 80. The other Raiders were in the 60-70 range or so.
I think perhaps the system might try to adjust the difficulty based on levels as well as MMR, so that a lower level Antagonist might have stronger AI helping them, whilst a higher level Antagonist will have weaker AI. I'm not quite sure how to test that, however.
Anyway, it still seems the best way to deal with this is to lower your MMR after a certain point, either by playing a friendly Antagonist or by forming a squad and throwing matches. High difficulty PvE matches don't seem to offer that much of a difference in rewards to offset the increased challenge anyway.