Dortmund has not been playing good in any of the competitions. They got punished in the DFB Pokal and were kicked out against Stuttgart and that game revealed all the weaknesses Dortmund is dealing with. The Bundesliga is again revealing everything as they are just not as lucky all the time as they have been in the Champions League. I don't know how often it happened that a team qualified for the next round in the CL when they scored only 7 goals in 6 games and were in one of the strongest groups of this season. Dortmund has played several games they should have lost, but didn't because their opponents were too stupid to score. I doubt that they will stay in the CL for two more rounds. Eindhoven is still doable for them, but I doubt it will be a long adventure for them.
Dortmund's performance is really bad this season, even though they are currently in 5th place in the standings, I also see that they will not have the potential to advance further into the top 3, even in the UCL, I am very sure that they will not be able to compete further.
The issue that is currently spreading is that Bensebaini (Dortmund defender) really wants to leave Dortmund and go to Manchester United in the January transfer market, to be honest, his contribution is quite big in maintaining Dortmund's defense this season, this is really a tough challenge for Dortmund, Dortmund will definitely sell him, because Dortmund management does that quite often (selling their good players).