The duo, both Supercars champions, ran in close quarters on the exit of Turn 1 in a frenetic start to the third race of the Darwin Triple Crown yesterday.
The outcome was Whincup being run wide and dropping multiple places.
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Immediately after finishing the race, having recovered to third, he recounted being “absolutely cleaned up” in an apparent reference to Courtney.
“I can't remember the last time someone has just opened the wheel up like that and just fed me off,” said the #88 driver.
Courtney went on to finish the race fifth, completing a solid weekend at the Top End involving a hat-trick of top 10 results.
The 40-year-old though was bemused when prompted about Whincup's grievances.
“I don't know what Jamie is complaining about; it's called racing, not following,” said Courtney.
“He was on the outside, so if you're on the outside there's not a lot of room there.
“But yeah, I don't know, I didn't think anything of it.
“He's got something to whinge about because his team-mate [Shane van Gisbergen] is beating him and I suppose he's blaming that.”
Whincup had earlier on Sunday exchanged praise with Chaz Mostert after their Race 13 battle for third.
More broadly, Courtney was pleased with his weekend's work, which has elevated him to ninth in the championship.
“Finishing the weekend with a fifth place was solid. It's not great, we obviously want to be further up, but it's solid,” he said.
“We're moving forward and progressing each time.”
Tickford Racing team-mate Cameron Waters was a little more reserved after experiencing his worst qualifying event of the season.
“We've had two probably bad rounds for pace with Tassie and here,” said the Monster Energy Mustang driver.
“We just couldn't really find what we were lacking all weekend.
“We qualified seventh and 12th and that's pretty bad for our expectations.
“We managed to race forward in that one [Race 14] which was nice, but it's not good enough really so we'll go back to the drawing boards when we go home and we'll work out what we have got to do to make these cars go a bit quicker.
“It's a long old year so it's not over yet.”
Waters is fifth in the championship, 297 points adrift of leader van Gisbergen.