Watch from the 1 hour mark. CB's letter to MWT. He says he comes out of prison in Dec 2006 "and from that point on, he does not return back to Praia da Luz"
Yes, the phone does not necessarily identify the user. But if the Prosecutors can prove he was the user of the phone prior to this - which it appears they can - the court doesn't just give the benefit of the doubt to the defendant.
Phone evidence plays a major part in court cases nowadays and it is generally accepted that the phone is assumed to be with the owner unless they can provide a plausible explanation.