The 18-year-old was sent off by referee Michael Oliver for a challenge on Matt Doherty, which was deemed 'serious foul play.'
Although the red card has been overturned, Arsenal's players are accused of breaking FA rules by surrounding Oliver.
Jurrien Timber received a yellow card for his protests, and Arsenal went on to win the match 1-0.
The club has until February 3 to appeal the charge.
"Arsenal FC has been charged after its players surrounded a match official during their Premier League fixture against Wolverhampton Wanderers FC on Saturday, 25 January," an FA spokesperson said.
"The club allegedly failed to ensure that its players did not behave in an improper manner around the 43rd minute. Arsenal FC has until Monday, 3 February, to provide a response.”