So I just finished the side-quest "Human Error," and I'm left feeling... confused. I found the compound and quickly proceeded to wipe everyone out, thinking they were trying to locate synths in order to kill them, or send them back to the institute. But their logs seem to suggest that they are definitely anti-institute, and the marker above the door seems to suggest a Railroad affiliation. My character has sided with the Railroad- did I just slaughter a bunch of my buddies by accident? If so, I feel slightly bad, but their methods still seem to not justify their cause...

If you actually do the quest in Covenant you'll end up either killing everyone in town like you already did or sparing them at the expense at someone else's life.

That being said, I believe by doing a particular Railroad quest, you stop the covenant quest from even triggering..

I think some of the companions reactions to this quest are a little off.

For Danse, he hates it if you let them live, despite the fact they've made great progress with the SAFE test, and have used it to find several synths.

He also dislikes it if you try to save the supposed synth woman. You can't win with him on this one.

This being pre Blind Betrayal Danse. If it was post these reactions would make more sense.

Covenant is pretty much the Commonwealth's Hackdirt.

Eerily enough, the women you can save from their cells actually does have a synth component on her...

Personally when it comes to mentally and physically torturing innocent people, regardless for what purpose, is always wrong in my book.

I, too, picked up the affiliation of the Covenant with the Railroad and it was the main reason for me not to side with that faction lateron.

I compare Railroad with PETA or Greenpeace in real life; trying to achieve an (essentially good) goal with such fanaticism that they would even put ethics regarding human life aside if needed/convenient.

Actualy the responce makes perfect sence, Danse in general is a good pearson/synth and methods used on improving SAFE test are barbaric and no decent pearson cud approve of them(physical/psyhological torture, murder of innocents etc... and we are not talking about just synths here since their test actualy has relativly low succes rates theres plenty of humans that get killed and tortured as well, not to mention that Covenant people will wipe out entire caravans etc for capturing one suspected synth so rly any even half decent companion should hate you if you let them live) now about second part of his responce Danse is loyal to BOS and their policy on synths is extermination and thats where the second part of his responce comes from.

And finaly to answer to original OP yes they are anti institute but they are also a bunch of murdering tortures so they deserve to die, not sure about railroad marker but knowing what Covenant people do it wud be hard to belive they wud be allied with railroad unless they are infiltrrating it:)