So it WAS Ben! And I think it's going to be Ben who is charged and remanded in custody too. As it stands, all the police have (as we're about to find out next week) is the taxi driver Lauren tracked down, who positively identifies Ben as being seen with Lucy near the time. Jay is Ben's alibi, and vice versa, so to go from that positive ID to a formal charge, they're going to need something more.
We know from the spoilers for next week that the charged suspect's family turn their back on them too, which is something Phil would simply never do, not even for Jay. So could it be Ian and Jane who drop Ben into it with the phone and purse containing Ben's fingerprints and it's that family walking away from Ben? DTC did say the storyline was going to get very dark for the Beales after the reveal...