When the situation on the beach had been stabilized—however briefly—she’d probably dragged him into the bubble.  Maybe she’d had help.  Or, maybe her weird tractor beam was strong enough.  Once he got to the ship, they’d probably put him in a stasis field, and then transported him here.  They might be examining his personal belongings—such as they were—they could even be holding them until he agreed to cooperate.  It didn’t seem to be their style, but it wasn’t too unreasonable to think that the rules might have changed a little bit when Lyra was threatened on the beach.