These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Alternative Character Interpretation: The Jovian Republic is commonly given this treatment. Tyrannical assholes who Put On The Reich to keep their people down and kill anyone who doesn't agree to their creed, or the defenders of humanity and the only voice of reason in a world of nanotechnology and genetic engineering gone mad?
Consider this: Your house has just burned down. While standing in front of the ruins, the ideas of various members of your family mostly range from "Everyone should have access to as much fire as they want - they'll surely not do anything immoral and/or stupid with it" over "Hey, we could build a new house by selling fire to those who can afford it!" to "I think the problem was that we didn't have enough fire!".
The Jovian rank-and-file is entirely sincere. The Jovian leadership, on the other hand, are a bunch of hypocrites who are all 'Fire for me but not for thee!', while pretending to be 'Only we can protect you from fire!'. Which means DMs have to do more than a bit of rewriting to make the Jovians a genuine 'Hey, they do some disturbing stuff but they still have a point!' faction. Which is annoying, because they're supposed to be useable as that faction right out of the box, but the secretly transhuman leadership in canon gets in the way of that.
Amusingly, the "fire" argument is mostly a Red Herring. While the TITANs did massive damage during the Fall, the Fall itself was mostly a result of humans finally destroying themselves due to human nature, pushing each other to the brink of war and armed with technology that could cause tremendous destruction. In this case, everyone's arguing over fire when in fact everyone who lives in the house is a raging pyromaniac.
Mary Sue Topia: Anarchist habitats, thought thankfully the authors caught on by Rimward and tried add some depth.
Nightmare Fuel: As a horror game, it's to be expected. For example, during the opening fiction piece, one of the commandos the story follows has his head sawed off and carried away (Presumably to have the contents of the brain uploaded to some computer left by the insane AI that built it) by a combat bot, and another is disassembled molecule-by-molecule by a swarm of nanites.