The Grove Racing driver found himself among the lead group during the first safety car of the race, which led to an awkward exchange with Broc Feeney at the safety car line.
Feeney had pitted while Reynolds had stayed out, the former coming out of the lane as Reynolds rounded Hell Corner.
The pair crossed the safety car line almost at the same time, with Feeney very slightly ahead, before Reynolds blasted ahead of Feeney in the queue.
Race officials noted that Reynolds was under investigation before the restart, before slapping him with a drive-through for passing under safety car shortly afterwards.
He tried to redress with Feeney to avoid the penalty, but race control was insistent that he still needed to serve the drive-through.
That left Reynolds baffled, given he claims he had no idea who was ahead at the line and was relying on instruction from race control if he needed to redress behind the safety car.
"Normally you race to the line and [race control is] the judge," he told Autosport.
"This time they were just the executioner, there was no judge going on.
"You just race to the line. He's come out of pitlane, so my speed is naturally higher and I'm going to go past him anyway. I pulled in front and waited for them to tell me [if I had to redress].
"I was looking at him and I didn't know where the line was. I needed them to tell me what was going on and they didn't. It ruined our day."
Reynolds said he would mull over whether to tackle race director James Taylor over the matter.
"I suppose I can bring it up in the drivers' chat and hopefully they can pass it along," he said. "It's a pretty normal thing to swap the positions around under safety car. It's very easy to do."
After serving the penalty the car stayed on the lead lap, Reynolds and co-driver Garth Tander were able to drag the car back to fifth at the end of the race.
Still, Reynolds was left frustrated by a day of saving fuel and running long to try and offset the penalty.
"Our aim was to be best of the Fords, but to get our time back we had to go off-strategy, do super-long stints and save a lot of fuel," he said.
"And it's not ideal because the tyres wear out too fast around here. It was a very hard day. Trying to make lap speed and save fuel is not fun for any driver."
One thing Reynolds was impressed with was teaming up with 2007 champion Tander, a five-time winner of the Bathurst 1000.
"Having Garth in my corner was unbelievable, he's just so good," he said.
"Really cool to work with, I really enjoyed my time with him. It was awesome."
