When I worked in retail, I quickly learned all about "loss prevention," which is the program that most retailers undertake to try and (you guessed it) prevent loss or theft of product at whatever store they're running. Customer theft is obviously an issue anywhere you have merchandise sitting out in public, but an even bigger issue, surprisingly, is employee theft.
And Apple isn't immune: Recently, an employee allegedly stole up to 25 phones at an Apple Store in Charlotte, North Carolina. The phones were taken out of a back room over about a month and a half in December and January, with the employee apparently just taking them out of the store. The total value of the property stolen was $16,000. The article in the local paper doesn't say if the police have found the thief yet, though presumably Apple would have all of their information. (The employee in question "had access to the Genius room," but may or may not have been a Genius Bar team member.)
At the retail stores I worked at (GameStop and then Borders for a while), employees would have to go through "bag checks" every day, to make sure they weren't walking out of the store with product. I don't know about Apple's policies specifically (though I'll bet employees could fill us in on the comments below), but whatever measures were in place, it appears this employee was able to get around them.