The Serie A side have been under increasing pressure throughout the campaign, sitting 12th in the league.
But they have progressed to the UEFA Europa League knockout stages despite being booed off by their own fans at the Stadio Olimpico after the draw with Trabzonspor.
"We are all sorry not to get the results which we worked for. We wanted to win tonight to take the top spot," Petkovic said.
"I have to admit we deserve all the criticism we are getting. However, as I said we tried our best and maybe we were a bit short of luck tonight against Trabzonspor.
"I am aware of the fans and I accept all these whistles, but I didn't hear them during the game as I was focused on trying to get a result."
Petkovic felt his team deserved to win, saying the Turkish side came to Italy playing for the point they needed.
He admitted his team's confidence has been hurt by their string of poor results, with just one win from their past six matches in all competitions.
"I felt like they only came here to avoid a defeat because that was what they needed," Petkovic said.
"We didn't take any of the chances we created. I feel that this was because of a lack of luck and self-confidence. We have lost a bit of form and belief because of the recent bad results.
"Therefore I am not totally happy with the result tonight and not satisfied. I am especially disappointing at having missed out on the win we wanted to take top spot in the group."
