Cleared all the npcs defeated the ferengi captain and his standing in front of my swaying but i have no option to capture him.
I posted this in another thread but I had this issue too and there is actually an onscreen notification that tells you to tag mok for transport before you get him completely down. If he says "can't we negotiate" I think you've taken him down too far. I found the best thing to do is to use your team to take out the nausicaans and then put them on passive and handle mok one on one.
Had this happen to me too. Beaming out and continuing helped. Second time I staid close to Mok, and at some point as his health dropped, a "tag for transport" button appeared. I quickly tagged him and mission finished.