I think I really screwed up. I'm playing the game and I killed the Kobolds in the crystal room and I didn't pick up the stakes. Now they are gone. Help.

If you have ToB, use the TAB key to highlight items on the ground. It may have fallen in a hard to see spot. It is a quest item and shouldn't disappear like other items. Failing that, the CLUA console code for the stake is: misc6w

or you can use shadowkeeper to put some stakes in your inventry, ive found 2 sets of stakes in bodhí's dungeon... one with the kobolds and an other one ...?? dunno anymore

The stakes will definetly not dissapear. They are on the floor somewhere, or have been accidentally dropped somewhere, or accidentally placed in a container.

HTH