Mateta's first goal was originally ruled offside but VAR overturned the decision - despite some angles still seemingly showing him in an offside position.
Mail Sport exclusively revealed that the Foxes were challenging the Premier League over the image used to rule him on, believing it to be taken from the wrong moment.
Cooper said: 'We're over it now, it was an awful human error that we believe has been hidden a little bit.
Leicester City have accused the Premier League of a VAR cover-up after the VAR process used to rule Jean-Philippe Mateta onside for his first goal at the weekend
'We have seen images that show he clearly was offside, but they froze it at the wrong time - everything seen has been a false image.
'We showed the Premier League that they used the wrong image. We had a massive error go against us, errors like that shouldn't happen and it's why we're changing to the semi-automated system.
'We felt very let down by it. We needed to stand up for the club and tell the Premier League what we thought.'
Leicester's next game on Saturday sees them come up against Everton, who are also winless from their first four games.
Everton have themselves let slip a two-goal lead in each of their last two defeats - Antoine Semenyo, Lewis Cook and Luis Sinisterra scoring from the 87th minute onwards for Bournemouth before Ollie Watkins' brace and Jhon Duran's stunner handed Aston Villa three points.
Cooper is not underestimating the threat of Sean Dyche's side though.
He added: 'We're taking every game as it comes and treating them with equal importance.
'(Everton) have a lot of very good players and a very experienced manager. We have to focus on what we can bring. We're excited about the game and being at home.
'It's been a brilliant training week, I have to say, on the back of a difficult result and a really bad decision we've had to pick up with the Premier League.'