Hi,
the box was sealed and I have actually played the console and the controller has the LED at the front rather than the top.
You'd be surprised the lengths people will go to. Would not surprise me at all if someone had bought one just to stick their old (unused) controller in and get the new one and then return it.
Unfortunately they will likely want to replace the whole item rather than just sort out the controller :s I noticed the other day there are two slightly different box cover styles doing the rounds on the same PS4 pro SKU (fairly obvious when you have a pallet load of them) so probably an older variants of the package still in stock in some places.