Overwhelmingly the most common case is people accusing others of posting in bad faith merely because the other's view is so far from their own that they can't conceive of them having it for legit reasons. This is a reflexive reaction—a feeling that we all need to recognize and stop ourselves from expressing in raw form. When people vent it into comments, the result is either war between the two sides, or, if one side outnumbers the other, an ugly mob dynamic in which a few people are ganged up on for being different. Those few either leave, or they become resentful and break the site guidelines badly themselves, as a way of lashing back against unfair treatment. All these outcomes poison the community.
Not to pick on you personally—it happens because of how human nature reacts to the weird conditions of the internet, which we're not wired for. It is hard for all of us to grasp how large and diverse the community is, and how divided it is on divisive topics. Nationalistic themes are some of the most divisive ones, and unfortunately are growing more common these days.
As far as I can tell this dynamic has nothing to do with reality. Reality is that the HN community has millions of people, is diverse in many ways including internationally, and is divided on divisive topics. That is already enough to explain the comments that show up. But none of us is wired for dealing with that. We're wired for loyalty to our tribe, needing to feel safe, and suspecting outsiders.
It's painful to encounter a sharp opposing view, and people are angrily sharp on divisive topics. Reframing the other as a foreign spy or whatever insulates you from that. It relieves you from considering what truth there might be in that view, and reinforces loyalty to your own—at the cost of feeling surrounded by infiltrators and enemies. This is poisonous to thoughtful discussion, which depends on people being willing to open to differences and truths they may not yet see.
Since the actual phenomenon is vanishingly rare compared to the insinuations people make about it, we have a rule that users not post such insinuations without evidence. A feeling is not evidence. Even the sense "there are a lot of green accounts saying things I disagree with" is usually just a feeling, because we notice things we dislike more vividly than we notice anything else [1]. People on the opposite side have the opposite perceptions, but the identical feelings.
Notice how when people post claims about astroturfing, trolls, and spies on HN, they don't include links; just as when they make claims about "threads about $topic", they don't include links. Why is this? If the perception were of reality rather than a feeling, specific examples would always be available, yet in practice they almost never are. The discussion falls apart when specific cases are mentioned because (a) people never agree about those, and (b) such data as there is never supports the claim. The discussion always stays in a mist of generality, breeding bacteria of suspicion.
[1] Does anybody know or have a name for this bias? It's a huge factor in these discussions and it needs a good name.
Uh, confirmation bias? Your description is a bit off, it's not that "we notice things we disagree with", but that we notice things that confirms our previous beliefs, in this case that green accounts post opinions that you think come from spies or astroturfers.