Top-two finishers in the past four seasons, Dortmund are rooted to the foot of the Bundesliga table through 19 matches this season - and sit two points from safety in the German top flight.
The home fans jeered Dortmund following the final whistle at Signal Iduna Park, as they made it five straight league matches without success.
With only four wins so far this term, Klopp said the criticism - which prompted Hummels and vice-captain Roman Weidenfeller to speak to the supporters post-match - was understandable.
"We can be accused of anything tonight and it is all justified," Klopp said.
"Battling also means having the courage to take the right decision. We were missing that tonight.
"It hurts, no doubt. We are doing everything wrong at the moment. We are not making anything of our chances."
Hummels headed behind a goal to talk to fans after the final whistle, with Weidenfeller climbing a fence to get his message across while Klopp and the remainder of the playing group watched on.
Skipper Hummels said his players needed to grasp that the reaction was justified before moving on, with their next league fixture a trip to Freiburg on Saturday.
"If one is in this position after 19 games then it would be unacceptable not to have understanding for the fans' reactions," Hummels said.
