Refereeing body PGMOL has admitted Brighton should have had a penalty for Pierre-Emile Hojbjerg's tackle on Kaoru Mitoma in Saturday's game at Tottenham.
The incident was one of a number of decisions that went against Roberto De Zerbi's men.
Hojbjerg seemed to catch Mitoma in the second half but referee Stuart Atwell did not give the decision in real time.
VAR did not intervene and Brighton eventually lost 2-1 to Harry Kane's late goal.
BBC Sport understands there has been direct communication between PGMOL chief Howard Webb and senior Brighton officials acknowledging the mistake.
If Brighton had won the game, they would now be in sixth, a point behind Tottenham with two games in hand.
Following the game, Brighton captain Lewis Dunk was critical of the failure to award a penalty.
"I don't see what VAR is here for," the defender said. "You bring it in for big decisions and don't make big decisions. What is the point of it? He has clearly fouled him."
BBC pundit and former Premier League striker Chris Sutton said the visitors had been "robbed".
"Howard Webb will be apologising to them once again, of that I'm sure! Truly awful," he added.
PGMOL apologised to Brighton following mistakes in their game against Crystal Palace in February and it is understood it also did so around an incident involving Solly March in a game against Aston Villa just before the World Cup.
In addition, Brighton have asked for clarification around five key decisions taken at Saturday's game, which saw a further penalty claim when Dunk's shirt was pulled in the box, and two Brighton goals disallowed for handball.
Brighton are also looking for an explanation as to why De Zerbi was sent off as the club believe he was actively trying to calm the situation down when coaching staff from both teams had an altercation on the touchline.
Spurs interim head coach Cristian Stellini was also dismissed.
