It’s been a while since I last played but here is what I remember.
For the hidden achievement that says “witness a secret better left buried” under it, complete the tapir god’s request then go to the pond. You should get an option to explore the cave. When prompted, proceed further and you should find a feather, then you get the achievement.
For My Little Bletchley Park, this one I think is determined by how your prior interactions with Argos play out. When you first meet him on the second day, challenge the contract and pick the article that says “The Master and the Jailer are symmetrically bound by this article”, or if you have the Humanities or Leadership backgrounds, you can trick him. For the second challenge involving the sacrifice, when you get three chances to question his statements (five with Leadership), question the last statement that says “offer the sacrifice to one of the godmade shrines”. The day after you go out into the valley to retrieve the bundle, you should be prompted to make the sacrifice to one of the shrines within the hotel; Hermes, Hades, or Hestia, I don’t think it matters which one you choose(I chose Hestia). If you did everything correctly, then when he is attacked by the bull, you should receive the diary page. Translate the page to get the achievement. If it still doesn’t work after following these steps then I don’t know what else to do aside from just playing normally.
As for the last hidden achievement, I don’t remember.
P.S. I’m going off of memory so I might have made a mistake somewhere.