Raheem Sterling struck City’s winner on 97 minutes.
Howe said: “Our aim for the second-half was to kill the game. We’re not frustrated at the goal being scored when it was scored, but more up the other end.
“We were looking to counter attack and there was a foul given against Lys Mousset. He made a perfectly good tackle and then they went on to score from that attack.
“So that’s what we’re more frustrated about.”
He added: “I am really pleased with the players, they were dogged and disciplined.
“There was also a great atmosphere in the stadium so I thank the supporters for that. But we had our chances to win it too, so it’s hugely frustrating.”