As you mentioned in your post, this is a game bug and nothing to do with the trainer. There are several quest bugs you can run into that have been reported that cause the quest to either not complete or get suck in your quest log with the "!" and cannot be cleared. This is something the game developers will need to fix and I highly doubt there is anything the people CH can do about it.
I know this has nothing to do with a bug or problem with the trainer itself. I was just mentioning this as they have had trainers in the past that would fix a known bug in the game. Unfortunately, the game escapes me, but I am sure that CH could confirm it.
On another note, I read an article stating that Bioware is cataloguing a list of bugs and glitches and are waiting to release an update for the game, however, they would not provide any specifics and of course, this does not mean they will include a fix for this.
Regardless of what CH decides to do or not do, I just hope that Bioware will get all these bugs fixed before I beat the game...
(I'm actually trying to play my first playthrough all legit, I've always loved using cheats right off the bat, enjoying just the game play mechanics)
All answers are here