Khusanov escaped with a yellow card from referee Sam Barrott after bringing down Kevin Schade when he appeared to be through on goal.
City went on to win the game 2-0 and book their place in the semifinals.
Afterwards, Andrews described the incident as a "big moment" and suggested that Khusanov should have been shown a red card.
"It was a big moment; 15 or 16 minutes into the game," Andrews said.
"I am very quick to defend officials, but it's one I feel they didn't get right tonight and the explanation of it being too far from goal doesn't sit right.
"If he goes through it is an opportunity on goal."
After playing at the Etihad Stadium, Brentford are staying in Manchester ahead of their Premier League clash against Wolves at Molineux on Saturday.
They're set to use City's CFA training ground to prepare for the game.
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And when Guardiola was told about Andrews' assessment of Khusanov's challenge in his post-match news conference, he invited his opposite number to talk about it over coffee.
"Tomorrow at the training ground, I invite him to the café and we will discuss," Guardiola said.
City's win over Brentford was sealed after goals from Rayan Cherki and Savinho either side of half-time.
Cherki's goal was a spectacular effort from outside the penalty area which found the top corner. Guardiola was impressed with the strike, but not with the Frenchman's performance before he was substituted in the 66th minute.
"We are lucky to have players score these type of goals," said the City boss "After that he didn't play very well but the goal was fantastic. In the second half Rayan did not do the job he should have defensively."
