Cotton agreed it was disappointing his side allowed their hosts to come back from the 3-1 deficit.
"We knew they would come back out and take it to us during those first 15 minutes of the second half.
"That was a bad period for us and we struggled to compete with their pace and movement," Cotton explained.
"At the same time we showed good spirit and character to recover from a 4-3 deficit and secure the draw," the former All White said, referring to defender Aaron Jones' header from a 78th minute corner.
Midfielder Tom Biss' decision to change his flight to a Gold Coast holiday until after the game paid off big time. He scored his third consecutive goal in as many games and Cotton described the 32nd minute effort from 27 metres out as the Bay's "best goal of the season."
That goal put the visitors ahead 2-0 after former All Whites midfielder David Mulligan had scored in the 31st minute in his first outing against his former club at Kiwitea Street. Mulligan scored from a free kick.
Auckland City opened their account in the 34th minute when Cristobal Marquez found the net.
Then Sean Lovemore gave the visitors their 3-1 lead with a 42nd minute goal.
After several earlier misses Auckland's Emiliano Tade scored in the 53rd minute after a classy pass from Ivan Vicelich.
Three minutes later Marquez scored his second to tie the entertaining encounter up.
Tade scored his second in the 71st minute.
While Biss again impressed with his work rate, Cotton said another of the Bay's midfielders, Sean Morris, also operated well.
Cotton is rapt his team is unbeaten since he stepped up to the head coach role this month in the absence of Chris Greatholder who is taking a break until next month.
"We've played the best three teams too," Cotton said, referring to Waitakere United, Canterbury United and Auckland City.
His players have fitness schedules to follow during the festive season and they will re-assemble on January 6 to prepare for their encounter against the Wanderers.