La Liga leaders Madrid were awarded a spot kick by referee Alejandro Hernandez Hernandez in the 41st minute of their match at the Bernabeu after Casemiro was brought down on the edge of the area.
However, replays appeared to show that there was minimal contact with the Brazilian.
Karim Benzema stepped up to put Madrid ahead in the match with his 300th goal for the club, becoming only the fourth player to reach the landmark after Cristiano Ronaldo (450), Raul (323) and Alfredo Di Stefano (308).
The France international would go on to score a second late on, with Vinicius Jr also grabbing a brace for Madrid, who ran out comfortable 4-1 winners at the Bernabeu.
Valencia’s social media team were less than impressed by Hernandez’s refereeing performance and let their feelings known on Twitter after the match.
Referring to the popular Spanish television series Money Heist, they wrote: “The robbery in Madrid begins to be somewhat repetitive.”
Barcelona defender Pique took the opportunity to hit out at Madrid by posting a tongue-in-cheek reply to Valencia, warning them against speaking out against the league leaders.
He wrote: “Do not say it too loud that they are going to sanction you.”
It is not the first time Pique has commented on the officiating in Spanish football.
In February 2021, Pique escaped punishment after suggesting the majority of referees in La Liga favour Real Madrid.
“A former referee, I don’t remember who he was, said that 85 per cent of the referees are fans of [Real] Madrid,” Pique told YouTube channel Post United.
“It is a statistic you look at [and think], how can they not whistle in favour of Madrid? Unconsciously, but how are they not going to give more to one side than the other?
“I totally respect the professionalism of the referees. I know they try to do the best job possible, but when there is a moment of doubt…?”
Barcelona have asked a number of senior players, including Pique, to give up part of their salary this season to help the club reduce its huge wage bill.
Spanish journalist Lluis Canut claimed that Pique is still one of the highest-paid players at the Nou Camp, and remains on a salary of around £450,000 a week.
However, Pique took to Twitter on Friday to call out Canut with a message alongside his most recent payslip, which showed a 50 per cent reduction in wages this season.