Didn't cologne also have 8 regulars not being available for the match?
Dortmund didn't play better or worse than against Hoffenheim, Bielefeld or Mainz. They just didn't have the luck they had against Mainz and Hoffenheim.
Dortmund isn't an elite team for a while. Just look at this year's cup competition. Despite having pretty easy draws, they failed thoroughly. None of their exits was unlucky or undeserved.
Their position in the Bundesliga is actually pretty good considering their performances. There were years they played much better football and were much further behind.
One reason of course is Bayern playing pretty underwhelming since the winter break.
I think it's truly worrying how they ended up with the team they currently have despite their considerable budget at this point. Some of the decisions they made are downright terrible. Meunier and Can were purely big name signings and it should've been clear to everyone with eyes that they don't possess enough quality. Schulz has been absolutely terrible to a degree that you have to question the scouting. I think there are no excuses for these decisions, they should never have been made.
The rest is more ambivalent. You've got generally good players who are somewhat hot and cold like Akanji, Dahoud and Brandt and at least in case of the latter, they also have themselves to blame for it. Then some great talents like Bellingham and Reyna who cannot be blamed for being incosistent. Then many injury prone players such as Hummels and Reus but also talents who are slowed down due to it (Moukoko, Morey, Zagadou).
I hope they refocus on what made them strong in the first place. Screw those big name transfers and when you do sign players to immediately improve the squad, make sure you have a plan for them. Save the huge salaries for mediocre players and spank the cash instead on holding onto your top talents for as long as possible. Accept a transitional phase when you lose a player and others have to step up instead of spending it on immediate improvements who actually won't improve you and instead will limit your spending power for years to come because you can't ship them off since nobody will offer them a comparable contract.