The second and final part of Pedersen's review was presented to the council on Tuesday, including Warren's report.
Pedersen said he understood three vessels had been damaged in the last year while using the 350-tonne travel lift at Vessel Works.
Those incidents and others caused some stakeholders to doubt the skill level of the people running Vessel Works.
Warren found Vessel Works was overall professionally run. In his experience, accidents happened occasionally in all boat haulage yards.
"Overall, I find very little wrong with the operations of the facility, apart from some personality conflicts, and minor communication issues with some customers."
He made a handful of process improvement recommendations to reduce risks.
Pedersen said Warren's conclusions should satisfy the council the Vessel Works team was technically competent.
In Tuesday's meeting, Paul Davidson, council general manager of corporate services, said issues had been raised about Warren's "independence".
The conflict of interest included a previous contractual relationship between Warren and Wardale in Auckland. Warren also consulted on the procurement of the travel lift.
Davidson said the conflict was acknowledged before Warren was hired and the pair had no current contracts or ongoing work.
Davidson said Pedersen and the council had trouble finding any marine professional with the experience and independence to do the review. The search was delaying the report so they went with Warren, who had a 17-step plan to how he would approach the review.
Councillors raised concerns the conflict would cause some to perceive the report as biased. Councillor John Robson said Warren did not speak to some key stakeholders.
Davidson said Warren discussed who he should speak to with Pedersen. The process Warren took would be talked through in detail with precinct stakeholders at a meeting on Wednesday of a new advisory group.
Contacted for comment after the meeting, Warren said he disclosed the conflict and fulfilled the obligations of his brief.
Wardale referred questions to the council. In a written statement Davidson said the council and Pedersen considered the conflict and believed it would not affect Warren's ability to provide technical advice.
In their previous contract, Warren was a general manager at Panuku Development Auckland when Wardale was a contractor.
Establishing the precinct advisory group was a recommendation in the first part of Pedersen's review, released in July.
He looked at whether the council had lived up to undertakings it made during the development of the precinct.
He found the council was generally delivering well. There was less "non-exclusive seawall berthage" than in the initial 2014 design, but changes were normal over the course of a long development.
He recommended the council consider not selling one lot in the precinct and consider setting it aside to "protect non-exclusive access to the water". He noted the council had also agreed to pay for new 20m wharf.
The second part of the review looked at concerns around the operation of the precinct.
Pedersen said the council should take seriously feedback that the Vessel Works team were difficult to deal with, and work with the team to improve customer service.
He also flagged an issue with discounts to fees apparently being applied "ad hoc", saying it was unusual and the council should review how fees were being charged.
Council chief executive Marty Grenfell said that while many issues had been raised regarding the precinct, and improvements were needed, he did not believe any were "critical" enough to "change the way the current operation is happening".
He said the council had hired a contractor to manage the precinct contract and work sorting out issues and improving relationships and engagement between precinct management, users and staff.
