I don't really understand Steamworks, I don't how know how to view the XML achievement listing for the game, and I was unable to find anything useful on the Facepunch forums, so I can't quite confirm what's going on here. However, I did read something in
Mayhem Intergalactic's change log that hopefully provides a bit of insight into what might be happening:
No final decisions, besides "something reasonable". I'll probably either deprecate the old achievements (so nobody can achieve them unless they already have them; they'll then continue show up on Steam profiles, but not in-game), or adjust their descriptions to "Defeat the AI at the Medium level" or whatever the closest equivalent to "Highest" ends up being. (Either way, I will probably also add new "Highest" achievements, though perhaps not for Perfect since that's hard enough already...)
I've italicized the relevant part. What Chris is saying here is that he may deprecate old achievements so that they can no longer be obtained and won't show on a person's profile, but those achievements would still exist internally. I think that's what happened with Garry's Mod. Killed 1000 Baddie and are you the real garry? probably still exist, but are not visible normally. If I knew how to view the full XML list of achievements in the game I could confirm or deny that story, but unfortunately I can't right now.
This problem could probably be solved with some sort of override that would prevent certain achievements from showing up on Giant Bomb, but it's not exactly a high-priority task.
The question mark icons on the other hand is definitely a Giant Bomb problem. The icon in question is for achievement 29574: Dollhouse; but it's not even the correct icon, and the exact same icon (
1130340) is used for every achievement between
29567 and
29574.
