at the end of the 2nd mission in the carrier and after killing all the guys in the top and dropping the boat.....i get in and try to leave and all the guy says is that i have to look for the girl and that i should go back into the carrier and look again....ive been to all the rooms and i found nothing.....when i try to leave a heli comes out and snipes me!!! is there something i have to pick up????

After climbing the ladder from the main deck, you should have found a room with a single merc. After shooting him, there should be a cut scene, where you see Val's ID etc on a table. You must trigger that cut scene before the mission is accomplished.

You cannot just shoot him and move on. You need to approach the table to trigger the cut scene.