Ormion,
Once I bought SEALED X-Dreams's double best of album from psyshop. It turned out that disc 2 wasn't disc 2 but disc 1 again! I returned it to them and sent me another, but of course had to pay the postage for sending back to Germany.
A missing CD inside a sealed package is another thing though. The store can have sealing machines too mind you. I mean not a second hand store, but an adequately updated CD shop can have it. It's not rocket science.
And, it's much easier to reseal digipaks. Most Jewel Cases which are (really) factory sealed have the seal squarish at the corners and the plastic is generally thicker and you can never duplicate that. But on digipaks the seal is thinner and can be fairly easily resealed without arising suspicion unless scrutinised prior to opening.