The Triple Eight driver's impressive run of eight consecutive top-five finishes came to an end on Saturday.
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A pit stop mix up cost Whincup 10 seconds when an air hose was not correctly connected, preventing the car from being jacked up once the car stopped in the pit bay.
As a result, Whincup managed to recover to 20th but lost crucial points to McLaughlin who won the race.
Whincup challenged for the victory in Race 16 on Sunday before sliding to fourth at the chequered flag.
The 34-year-old felt, both he and the team, made errors during the weekend which have ultimately proved to be costly.
“We have made mistakes this weekend both driver and engineer and we will learn from it and put a plan in place to make sure it doesn't happen again,” Whincup told Speedcafe.com.
“They (rough weekends) shouldn't happen, we didn't do a good job this weekend there are no excuses. We didn't do a good job and we paid the price for it.
“After three rounds and scoring maximum points here and there we have thrown away a good 120 points.
“It is disappointing but that is the way it goes and we have just got to make sure it doesn't happen again.
“I think we had a car good enough to win but we didn't. We went aggressive trying to get the win and the end result was we missed the podium.”
Although frustrated to lose ground, Whincup remains confident he can once again build another consistent run to boost his title hopes having seen his rivals all suffer difficult rounds this year.
“For sure I'm confident we can get back on a consistent run but I'm just disappointed about Saturday,” he added.
“It is far from over, we just don't know how damaging Saturday is going to be for the big picture, hopefully not.
“We won't know what goes on until the end but it feels damaging right now.”
The Virgin Australia Supercars Championship continues at the Red Rooster Sydney Super Sprint from August 18-20.