"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.
Swansea looked set to end City's four-pronged pursuit of honours when they took command of the tie after Matt Grimes converted a 20th-minute penalty and Bersant Celina finished off a fine move by curling a shot beyond Ederson nine minutes later.
"If the second was not a penalty and the third offside, I'm sorry", said Pep Guardiola, Manchester City manager.
"We will analyse the game - we deserved to win the game by far - but to win in that way, I'm sorry".
After the break, City were struggling to find a way back into the game and it was after the introduction of Raheem Sterling and Sergio Aguero from the bench that they started to threaten.
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This was against West Ham, for whom Michail Antonio equalised on a night when Liverpool frustrated their travelling supporters at London Stadium.
Last season, City were embarrassed by League One Wigan in this competition in the fifth round and this was a game which had a similar feel from the early stages.
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The Red Devils were handed a red card following a reckless challenge by Victor Lindelof on 83 minutes, but the Video Assistant Referee overturned decision and the defender was only handed a yellow card.
"We are so happy", Silva said.
Guardiola said: "You have to say congratulations to Swansea, it was incredible". I don't like to win in that way. "It could have gone either way, Congratulations to Swansea who played very well and made it hard but we kept going, pressing and eventually the goals came".