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.
I did the same thing...killed him. I assumed the game would consider that a "defeat" and beam him out. Silly me. Anyways...instead of beaming back to the ship & starting over (I almost had a fit when I thought of that)...I walked all the way back to the beginning. Then I started walking back to his spot, and I saw all the red dots...sure enough, he and his guards were back.
I don't know if that itself was a bug...but if it was, I'm not reporting it cause it saved me from starting all over....lol