Incorrect penalty decisions were made by the video assistant referee in all three of Thursday's games, the Premier League has told BBC Match of the Day.
Bruno Fernandes won a spot-kick which he scored in Manchester United's 3-0 win over Aston Villa.
James Ward-Prowse hit the bar after a disputed penalty as Southampton drew 1-1 with Everton.
And Tottenham should have had a penalty for a Joshua King shove on Harry Kane in a 0-0 draw with Bournemouth.
The Premier League confirmed United and Southampton should not have been given penalties, but Tottenham should have been awarded one.