It seems to have become quite a popular past-time in late 2008 to troll the directories forums over at DigitalPoint and fight with directory owners.  My guess is that most of the trolls are folks that have tried to run their own directories but failed and now they are jealous of others that are successful.  Here is some sample post titles of trolls:

directory submissions caused massives serps fall - proof inside

Besides the fact that the OP offers very little data the main premise of it is all wrong.  There is no way Google or any other search engine will penalize a site for being listed in free directories.  It would be too easy to bomb your competition by submitting their site to some free directories.

One of the biggest problems with trolls is that members feed them by posting in their threads, thereby keeping the threads alive.  If you see a troll post just red rep and move on.