This is the main problem. Dortmund lost points against a relatively weak opponent. Even if Dortmund had lost points against Freiburg or Leverkusen, I would have said that Dortmund had some chance of winning the title. Now that their performance has been erratic, it will take a long time for them to get back on the winning track. In the future they will play against Frankfurt and Freiburg. They will also fail to score full points from these two matches.
It is chronic problem of Dortmund in past several seasons. They did not manage to maintain their good performance in a whole season while Bayern can do it. So Dortmund always end seasons with less total points than Bayern. They did not win title because of an unstable general performance and in this season, this chronic problem occurs again.
I don't expect Dortmund will fix it with players they have and with very stable and dominating performance from Bayern, Bundesliga trophy will likely be taken by Bayern, one more season.
Freiburg or Leverkusen won't be able to do better than Dortmund in my opinion.