Anyone having problems finding the last cypher? There is a hard anomolous site with two steps but I am unable to do anything other than leaving the site.
Aren't anomalous sites denoted by the purple triangle hologram looking thing? I don't think those give cyphers. You've gotta look for exploration sites. They're those buildings that give sector bonuses like +20 resources and an attribute to units you build. They are diamonds on the map with a black/grey fade background and a red outline if you haven't cleared them.
If you haven't cleared them, you can scan them for cyphers for a turn then win the fight next turn and claim a cypher. If you've already cleared them I think you have to fight the new chaos enemies and maybe you won't always find a cypher.
As for you not being able to do anything with your anomaly site, that might be a UI bug that's affecting things like clearing hazards, annexing sectors, entering exploration sites, etc.. If you reload your game it should be fixed!
I also found out that the cypher collection mission that If you don't collect all 3 on one planet and do another grail mission on another planet, it still holds it's progression.