Ibrahimovic was on target at the Stadion Pod Goricom but it was not enough as Sweden were forced to share the spoils with Montenegro away from home in Group G.
The 33-year-old made his comeback to the Swedish national team after missing the past two Euro 2016 qualifiers due to a heel injury, opening the scoring in the ninth minute for his 51st international goal.
However, Sweden were denied late on as Montenegro striker Stevan Jovetic converted a penalty with 10 minutes remaining.
Hamren felt Sweden, especially their defence, did not make the most of Ibrahimovic's return.
"I was worried about Ibrahimovic's injury but he managed to play the whole game," the 57-year-old said.
"We had Ibrahimovic back after two months' absence and we had to exploit that, but we didn't."
Sweden - unbeaten after four games - are four points adrift of group leaders Austria.
"I am disappointed with the result. We took an early lead, then controlled the game. In the second half we hit the post," Hamren added.
"At the end of the day I am not satisfied with how my defence performed. Only when we conceded the equaliser did we go on the attack, but it was too late."
