This is a copy of advice that's both in CWM forum and EG forum
>>If you get this mission run a search for "oveon" (I think it means transport in gaalian). You'll get a list of the 30 nearest Gaalian transports. Your target will be in the designated system when the mission begins. ...usually only one ship fitting the description.
Run that search before you leave the planet you got the mission from, then you'll know his name. <<
Usually when you get there the ship has "jumped" to another system, but he'll be back just in time so that you've enough time to shoot him down, just hang around the jump-point.
Or you can cheat a little by saving the game, flying to the system where he should be and then checking where he jumped. Then reload and fly directly to the system where the target is jumpping into then you have a little more time to shoot him down.
PS. I'm really surprised that they haven't fixed this - it was maybe the most widely known bug in the 1.3 version.