Despite dominating possession throughout proceedings at the Imtech Arena, Klopp's men were left frustrated by a spirited rearguard display from the hosts.
Switzerland international Behrami put in a particularly physical performance and was booked in the 31st minute before being substituted. However, replays suggested he was lucky not to see red for seemingly striking Mkhitrayan after two minutes.
He was quoted by Sport 1 as telling reporters: "Normally, that would be a red card.
"I don't know if it's because he's not played in a while or whether he lacks the coordination or whatever - it was enough to take the arm up and hit in the face Mkhitaryan.
"Whether it was intentional or not, we do not care at the moment."
The stalemate leaves Dortmund seven points adrift of the Europa League places and nine adrift of UEFA Champions League qualification.
Asked about Dortmund's by the club's official website, Klopp said: "There are many positive aspects. Even if it does not feel like a point gained, that will come later in the evening.
"We have kept Hamburg at a distance and added one more point to our tally.
"We had a relatively large amount of superiority but could not capitalise. We found ourselves in the wrong positions at the wrong moments without putting too much pressure on up top.
"We have taken a point which is a positive and no one is injured which is a mega positive, but anything else is just so-so."
