Mikel Arteta's side recovered from a slow start to see off the League One side 3-0, with Eddie Nketiah scoring twice after Mohamed Elneny's header had broken the deadlock.
With the contest goalless in the 34th minute Arsenal believed that they should have been awarded a spot kick when Albert Sambi Lokonga's strike hit the hand of Elliott Moore and went behind for a corner.
Replays showed the ball clearly striking Moore's trailing arm as he fell to the ground to block the shot, leading Arsenal players to immediately surrounding referee David Coote.
Lokonga, Kieran Tierney, Elneny and Gabriel Magalhaes were shown asking the question to Coote, who waved away the appeals, and there was no VAR available to review the official's decision.
A statement from the FA announced that Arsenal had been accused of improper conduct, only a week after an identical charge for similar behaviour in their Premier League clash with Newcastle United.
"Arsenal FC has been charged with breaching FA Rule E20.1 during its tie against Oxford United FC in the FA Cup on Monday January 9, 2023," the statement read.
"It's alleged that Arsenal FC failed to ensure its players conducted themselves in an orderly fashion during the 34th minute, and the club has until Monday January 16 2023 to respond."
Last Friday, Arsenal were slapped with another breach of the improper conduct rule after their zealous appeals for a last-minute penalty in their goalless draw with Newcastle, where Granit Xhaka's cross was blocked by the arm of Jacob Murphy.
Referee Andy Madley waved away the appeals, as did VAR official Stuart Attwell, and the Gunners were also denied a spot kick when Dan Burn appealed to grab hold of and haul down Gabriel inside the area.
Arsenal manager Arteta labelled the decisions "scandalous" after his side dropped two points in the Premier League title race, telling the press: "It's not about stronger, it's two penalties. That's very simple. I'm talking about what I've seen now. It's two scandalous penalties.
"We had a lot of situations around the box to do better and then those penalties. Both of them. It's not particular. It's a penalty or not a penalty and these are both penalties.
"I feel the team was on top, we were chasing it, we really wanted it. You could see the team was doing everything to win it. We lacked that in the final third and then we lacked the two big decisions obviously."
Arsenal will face Manchester City in the fourth round of the FA Cup after beating Oxford and resume Premier League duties away to North London rivals Tottenham Hotspur on Sunday afternoon.