Swansea said the club was set up to use VAR given their history of being in the Premier League between 2011 and 2018.
The City manager's decision to name Sergio Aguero and Raheem Sterling among his substitutes at the Liberty Stadium in south Wales looked set to backfire as the Championship side made the most of their absence to surge into a surprise two-goal first-half lead.
After Bernardo Silva's superb finish with the outside of the boot got his side a foothold in the match, Aguero was presented with the ideal chance to draw City level after Sterling had been felled in the penalty area.
But United were unable to match their city rivals, slipping to a 2-1 defeat at Wolves to hand interim manager Ole Gunnar Solskjaer a second consecutive defeat.
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Guardiola said: 'If it is not a penalty, and it is offside like the people say, I'm sorry.
"We are in the dark ourselves over the non-use of VAR here and that it would only be used in Premier League stadiums", the spokesman told Press Association Sport.
Aguero completed the comeback with two minutes remaining, when he stooped to head home Silva's cross from the left to keep City's dream of lifting four trophies this season alive. "The performance was one to be very proud of".
"We are so happy", Silva said. "We know every game we lose, we lose the competition".
"I'm here until the summer, we've got loads to play for in the league and the Champions League".
But they were silenced temporarily when Etienne Capoue slotted Watford ahead in the first half to put the hosts ahead.