Derren said:
Player: I open the door [makes passive check->fails]
DM: You see an empty room
Player: Really? [makes active check->success]
DM: No, there is a pedestal in the middle of the room with a big, fist sized to be exact, cut gem in the middle of it.
Not to be mean, but this is why Spot and Search checks have a bad rap in 3e. Making players roll to see obvious things is one of those things that makes my head hurt (and makes me want to hurt the DM I'm playing with). If there's something obvious in the room, the players need to be told about it. If they say "I look under the bed" and you know that there's a box under the bed, making them make a "Search" roll to find it is not only irritating, it's just plain weird.
Now onto the actual example you're butchering here - the Perception check specifically says "you spot the strange gem". It doesn't say "you see the pedestal". There's a lot of leeway in the reading of "you spot the strange gem" - the way I'd run it would be along these lines:
Me: ... in the center of the room you see a large pedestal engraved with skeletal figures around its base. Atop the pedestal is a large mutl-faceted crystal.
Player: I want to examine the crystal
Me: Does that mean you're going to try to pick it up?
Player: NO! I'm not even leaving the doorway - I just want to see what I can tell from here.
[Make secret Perception check or have player make perception check - it fails]
Me: It looks like it's probably too big to be a gem, unless it's a really expensive one. But you can't really tell much more than that from where you're standing.
[or, if the Perception check succeeds]
Me: There's something ... strange about the crystal. At first you thought it was reflecting some of the light from your torches, but as you inspect it, you could swear that it's actually glowing on its own. It's definitely weirding you out a bit.
Now, on the other hand, given the text description of the trap, I'd probably make the gem much smaller and embed it in a statue. That makes the reading of the line "you notice the strange gem" make a bit more sense - if you're standing 25' away from a large statue, you may not notice that one of its eyes has a small blue gemstone in it. But as it stands there's nothing wrong with the trap description - it just assumes that there's going to be a DM there to interpret it for the party at the table.