City eventually won 3-1 to reach the final 5-1 on aggregate.
Howe later said: "It was the start we didn't want. The first goal, Dan (Burn) has gone to clear the ball and it's gone off their attacker and gone in.
"That sums up the start of the game we had. It was the opposite of what we wanted and it took the game away from us."
On Newcastle's finishing, Howe added: "In both games if you look back. We are frustrated we only scored one goal in two games. We don't feel we should have lost the first leg 2-0 on the balance of opportunities created.
"It could have been different but we accept the reality. The last thing you want to do is have to chase a game. We were going for the match, we were trying to attack."
On Anthony Gordon's injury, Howe offered a positive report: "It looks like hamstring injury, I don't think it looks too bad."