What you could do is alter one of the items you loot off the body of the player, so it's identified description may note something about a possible tie-in with the twisted rune. Another option could be to have a note in the Twisted Rune area which lists a set of unique equipment that a certain infiltrator is using, has been issued and have those items show up on one of the enemies in the Slavers compound. More on this later.
Now is later: I recall that one of the fighters in the Twisted Rune encounter doesn't have very good gear. If there was some way to allude to the fact that some of his normal gear is being used by one of the infiltrators, such as the guy weilding the Celestial Fury that could be the tie-in. That may be a bit too heavy handed, so you could also have some sort of item requisition list keeping inventory of what types of items have been issued. Another thing that could be done, is have one of the Twisted Rune members make a comment about how when this is done, they'll have to make sure that their agent didn't allow them to be traced back there. I don't really like this one, since normally Twisted Rune agents don't even know that they are working for the Twisted Rune.
Another idea, would be to do something with the empty potion bottles. Perhaps there could be some empty potion bottles found in the Twisted Rune chamber, as well as some full ones of the same type. It could be some sort of drug which is used to give the slaves more energy so they can work harder, while depressing their spirits so they consider their situation more hopeless (idea stolen from Robin Hobb's Farseer novels). You could add the description to the bottle(s) found in the Slaver's Compound, possibly add some sort of dialogue, or clue that the agent had recently 'obtained' some of this drug, and find that the source of the drug is with the Twisted Rune who are supplying their infiltrator.
Another thing that could be done, is to have the person who meets you ask you who you got that rogue stone from, with possible responses including the one which provides the linkage. Perhaps have the response to the "I got it from the guy in the Guarded Compound" answer be something like "I see....", (or another response which hints at a connection with the guy who drops the rogue stone there) while the response to the other answers are something like "Just a random fool blundering where they have no business being".