Warning: spoilers ahead.

There's only one puzzle that is really poorly designed (IMO, at least). That is simply a design flaw. The puzzle is simple enough (re-arrange some bones to match a fossil you find in the same location), but there's no feedback from the game to let you know you've succeeded. So, you might think you have it wrong and keep on and on. All it would have taken was for Lowe to say, "That's it!" and exit the puzzle.

Perhaps the most infamous puzzle is a trap you have to build to capture a small alien creature. The in-game hint suggests you need to find some bait or "be a sheepdog," but it's not clear what that means. Again, the developers wanted you to do approach the puzzle in a unique way, but didn't make it clear enough what was called for. The hint should have been something like, "Maybe I could hide over there and walk the other way around" or something to that effect. Granted, that may have been too easy, but just "be a sheepdog" isn't clear enough (and even misleading).