In the Foundry quest, did you checked the security tapes? IIRC, there is a sec cam in the visits room. Your conversation with the agent could have been recorded, and that's why it counts as a "moderate success".
With the Lenox quest (which is the trickiest one IMO), I was able to recognize the cause of death because I passed the Biology check for the corpse. If not, you can ask Pasquale about checking the corpse and he'll notice the strange wound, which is one of the proofs, but to convince him to check it you need more evidence. Got the info from the ex-praetorian, I knew the name of Mordre so I had proof, and that was enough for me. I said it was Mordre because revenge motives, and gave him all the proof (his real name, the Spectre's methods, the info in the praetorian hard drive and the wound).
In the Hercules quest you can expose the guy by giving the info to the bartender or hijacking the JKK's streaming net (you need Hacking but I'll suppose you have it because basically Hacking/Lockpicking are mandatory in the game, regardless of build). Obviously the good way is with the JKK hack because that way more people see it. The terminal is in the Docks, I think that you have to go to the west and inside a building with hobos watching the terminals. There should be a ladder leading to the terminal's room.
I don't think they are bugged tho. There is just so many little details. The organization is very nitpicky for good reasons. They are extremely difficult, yes, but I like the quests precisely because secret factions should act like that.
