May want to check here, you could have missed something to complete a mission proper or it could be one of the many issues they are having with the DLC. As far as I know the trainer does not alter mission objectives so not sure why it would be the trainer.
Unfortunately, I've tried it that way as well. Doesn't work; I even tried acquiring 10+ perks without spending, to no effort.
On what distribution platform do you own the game? What's your game version?