I think the mission is called Raiding the Raiders. You need to find explosives and capture a ferengi captain. I have done this mission 2 times now, once by myself and once with a friend, and both times I had to defeat the ferengi captain twice before I could tag him for transport.
The first time you "kill" him he just stands there and wobbles like he is knocked out, but you can't activate him. I had to run back to the beginning of the area, so that the captain would respawn, then go back and "kill" him a second time before i could tag him for transport. This happened both times I did the mission. After you kill him the second time he will stand there and wobble like the first time, but you can activate him.
Actually, the second time I ran through the mission, my friend had set the captain on fire with a plasma grenade and instead of standing there wobbling, he ran around in circles. He stopped fighting and could be activated for transport, but he kept running around in circles. It was pretty funny.