A pair of changes to a $35 million-plus Miracle Mile project failed to receive Rochester City Council approval Wednesday, despite already being in place.

“Every development tradeoff was made against the city’s interest,” council member Patrick Keane said of changes to the new building that houses Avani Living Apartments, Fresh Thyme Market and Fiddlehead Coffee.

The two changes in question are the removal of a window in the eastside of the building and the placement of air-handling equipment in a planned patio area.

RELATED: Miracle Market changes get first nod

Keane said alternatives were suggested by the city’s Community Development staff but weren’t accepted by the developer.

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Miracle Market LLC owner Javon Bea said the changes were made due to requirements of Fresh Thyme and Fiddlehead, adding that at least one of the city’s recommendations would reduce parking spaces needed by the businesses.

Monday’s denial means Bae must revisit plans and likely make changes to obtain a certificate of occupancy, which is required to start receiving tax-increment financing payments that were approved by the council.

Council member Mark Bransford, who represents the ward that includes the project, said the developer’s changes don’t warrant requiring alterations since they were made to meet requirements of businesses that are benefiting the neighborhood.

“This is not a case of the developer thumbing his nose of making changes willy-nilly,” he said.

Council member Shaun Palmer also said neighborhood support shows the project is meeting local needs.

“If you have the neighborhood association that likes it, it’s hard for me to argue with that,” he said of the Kutzky Park Neighborhood Association.

Council member Molly Dennis said the issue goes beyond whether neighbors like the project.

The design was negotiated as an agreement between neighbors, the developer and the city before it was constructed. Dennis said the agreement is at the core of the matter.

“I believe strongly that this is an issue about a contract,” she said, pointing to the agreement that includes $3.5 million in TIF support.

“TIF dollars should go to companies and developers that fulfill their contracts,” Dennis added.

City Council President Brooke Carlson said she sees merit on both sides of the issue but added that she believes the developer and city staff can find a solution that will work for existing businesses and neighbors, while also bringing the project closer to the approved plan.

“I hope a different approach would be considered,” she said, joining the 5-2 vote to deny the acceptance of changing the official plans to reflect the current building.

Bransford and Palmer voted against the denial.