Dortmund are the engineers of their own downfall. I can remember those years when Dortmund were the only team giving Bayern Munich tough competition each season but those glory days are slowly disappearing because Dortmund turned their priority to be a business oriented club and selling out every top talent they get for huge profits not minding the competition ahead of them. Leverkusen have now stepped up to become the contender for Bayern Munich. They are focused on competing and winning trophies.
BVB keeps saying they want to perform at the top level in all competitions, but talk is cheap. It doesn't seem like they are willing to put the money where their mouth is and invest in top-shelf players to stop being a permanent underdog in the European cups, counting mostly on luck.
As I said before, to me it looks like the club is content with staying in the shadow of Bayern (and maybe now Bayer as well), and they're not willing to risk any money to take the club to another level.
But it works for them I guess. That's still enough to finish in the top of the Bundesliga and qualify for the UCL.