Actually, probably what happened is that some poor warehouse rep was scanning in devices and got an iPhone 5 return mixed up with an iPhone 6 return. So it's good that the OP sent the iPhone 5 back because someone else is probably being told that his device was never sent back (or that he sent back a 6, lol).
Yes, we were just speculating why someone might swap it out if it was in fact an act of theft, not what actually happened with the OP.