I had that with the 5S .. it disappeared just after it arrived in the UK and never made it to the local depot (so it was a carrier issue)
It took a week of constant calls to both UPS and Apple to get a new one sent out
They never found the original phone
From what I found out, they bulk sign the whole consignment in rather than the individual packages. Hence they could not say where mine was once it hit the UK only that it hit Customs. I believe the Depot itself over the 'call centre' as the information on the depot systems showed way more than the 'call centre' or 'website' gave.
Lets hope this year the phone does not go missing again
And this is why I do in store pick up.....