Courtney finished 17th in the 57-lap race, having struggled for pace in qualifying which left him 16th on the grid.
During the race itself he ran as high as 13th in the early stages, with a late pass on Michael Caruso stealing 17th on the final lap.
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The relative lack of pace came in stark contrast to Friday practice, where both Walkinshaw Andretti United cars were inside the top 10.
“We were a bit surprised, we've got to have a look at everything,” Courtney told Speedcafe.com.
“It definitely felt quite unique, so we'll just look over everything and see what happens because it definitely wasn't behaving the way it should and the way it has been.
“Through yesterday it was really speedy and then in qualifying something (was wrong) and then now it's sort of gotten worse.”
Walkinshaw Andretti United is understood to have experienced vibration issues with its front splitters on Friday.
A front splitter issue typically manifests as a vibration in the front end, something Courtney admits he experienced in Saturday's race
“There was a mad vibration in the front, so could be it, could be a number of things,” he said.
“We had a bit of everything going on. We'll pull it apart. We'll know more in the morning once the guys can have a look over everything and see where we are.”
It marked a five-place improvement for the Holden driver and mirrored the pace he'd shown during Friday's practice session.
The Phillip Island 500 continues on Sunday, with qualifying at 1040 AEST before Race 10 at 1350.