From the matches Ive seen Bundesliga teams are really sitting back against Dortmund at times forcing them to play in possession. Without Sahin, Gungdogan, Reus, they lacked that technical ability to break those teams down, and players were awkward trying to take on new roles.
Against Arsenal, they played counterattack, which didnt require that much heightened technical ability from the middle.
Once Sahin, Gungdogan and Reus are all back in shape and form, the team will go back to normal.