Unfortunately, there are a couple of items they forgot to mention.
1) It only works OOS, as while your IS, the freighter avoids collisions, and can't collect, where as when your OOS it has no problem.
2) The freighter has to SEE the rocks you want to collect.
Problem 1 is easy to deal with, just don't BE there during the process. A warning though, if you plan on returning to the sector, STOP this ship (give it a none command) or it's liable to slam into something when your presence returns normal flight characteristics to all ships present.
Problem 2, means you have to move the freighter near the brocken rocks, so that its radar can detect them. I suggest putting a Triplex radar on, as this will widen its 'visual' area nicely.
There has become an ODD problem, of rocks the ship wont collect. Even when their part of what you blew up.
Approach the offending rocks and shoot them, eventually you'll HEAR it explode, see little rocks form out, but the rock will appear to remain. This is a sign of 2 rocks occupying the same space. As such, the freighters cant touch either, so blowing both up is the only cure, then leaving and telling your ship to get the agitators.

Hope this helps.