I've heard an estimate that on many electronic production lines as many as 3-5 percent of components are defective. Additionally cars can be a harsh environment with temp changes and vibrations. Or maybe even a software issue that techs find easier to change out component rather then reprogram - but I doubt that.

On my 2002 car one of my Smart Key's had a grey plastic piece (located where the battery tray is found when the access panel is removed) was molded a tiny bit too thick. The thickness prohibited the buttons from making proper contact when pressed and resulted in intermittent working of the door locks when that key was used. I broke off a small tab on the grey plastic piece myself and the key now works flawlessly. But you said both your keys won't working.