Van Dijk, 34, had his equaliser in Liverpool’s eventual 3-0 Premier League defeat to Man City on Sunday (November 9) chalked off.
VAR came to the decision that Andy Robertson influenced play while stood in an offside position, and Liverpool have since contact PGMOL regarding the call.
Liverpool boss Arne Slot said it was "obvious and clear" the decision was wrong after the game, but PGMOL chief Webb disagreed on Match Officials Mic'd Up.
Webb said: "As the ball moves towards Robertson - three yards out from goal in the middle of the six-yard box - he makes that clear action to duck below the ball. It goes just over his head and finds the goal in the half of the six-yard box where he is.
"The officials have to make a judgement, did that clear action impact on the goalkeeper and his ability to save the ball? That's where the subjectivity comes into play.
"They looked at that action so close to the goalkeeper and formed that opinion.
"I know that's not a view held by everybody but it's not unreasonable to understand why (the officials) would form that conclusion when the player is so close to the goalkeeper, the ball is coming right towards him and he has to duck to get out of the way.
"They form the conclusion that it impacts Donnarumma's ability to dive towards the ball and make the save.
"Once they've made that on-field decision, the job of the VAR is to look at that and decide was the outcome clearly and obviously wrong.
"Only Donnarumma truly knows if he was impacted by this and we have to look at the factual evidence."