Focusing on the Champions League too much and having problems in the Bundesliga on one hand isn't very ideal for Dortmund at all. Dortmund's main target must always be to finish the season in top 4 at worst. Because the Champions League is like a tradition for Dortmund as they can normally finish the season in this area easily.
But right now things are going really badly for them about this topic. While Stuttgart and Leipzig are performing much better Dortmund will need to work much harder than this. As there is a long time to go for next round games in the Champions League Dortmund had better work on their weaknesses in the Bundesliga.
UEFA Champions League have made football to become very interesting and entertaining for we viewers, we can watch the substandard and crucial standards of every club in all categories, both elite and average at their peak. Finishing in top position is definitely for competitive clubs, they're acquainted with the system. Dortmund will lost one significant spot, either in UCL or Bundesliga, but I'm pretty sure they wouldn't settle for any loss in Bundesliga, that's one of the basic reasons they're fighting really hard to face their struggles. Borrusia Dortmund is not consistent as supposed, they're distracted because in bundesliga, they're struggling to win matches and currently ranked 5th position while in UCL, Edin Terzic and his team are enjoying football.
Talking about Borussia Dortmund and their different performances in the UEFA Champions League and the German Bundesliga, I don't think the club would deliberately want to do well in one competition and falter in the other one. The league campaign is often played almost all the weeks during the season and it takes many more number of matches to decide who will finish in the top four of league or even win the league which is absolutely contrary to what happens in the UEFA Champions League whereby a club only needs to play six games to either progress to the knockout stages of the competition or be eliminated from the competition.
Borussia Dortmund somehow prioritised and performed better in the UCL group stage because they knew that they were in the toughest group and must perform well to remain in the competition. Now that the group stage of the UCL is over, I think they'll shift their attention to the league and start to do well