Pique feels Barcelona deserved a spot kick, after Ferland Mendy appeared to pull down Martin Braithwaite in the dying minutes of the game.
However, referee Gil Manzano waved play on and VAR did not intervene in the decision.
Pique returned from injury but could not make Ronald Koeman’s XI for the game was only able to make the bench.
At the end of the game Pique was shaking hands with Real Madrid players when Modric noticed he was queuing up for the referee.
Footage picked up Modric mocking his the Spaniard, asking “You’re waiting for the ref to complain huh?”
But Modric’s comment did not, however, stop the veteran defender from asking the match officials some questions regarding some of their decisions during the game.
On the course of taking to the referee Pique got himself booked, picking up a yellow card despite not playing a single minute in the match.
Benzema opened scoring for Real Madrid in the 13th minutes and Toni Kroos doubled the hosts lead from a free kick but Barca pulled one back through Oscar Mingueza on the hour mark.
With the victory Real Madrid moved up to first spot on the league table ahead of Atletico Madrid on goal difference with Barca one point behind.