Arsenal progressed to the semi-final with a 1-0 victory over their London rivals.
Danny Welbeck scored the only goal of the game with his fourth strike of the season.
The one blow for Arsene Wenger’s side was that forward Olivier Giroud withdrew in the second half after picking up a hamstring injury.
And things got worse after the game as the two set of supporters tried to get at each other inside the ground.
Objects were thrown to and fro between the fans.
A row of stewards and police prevented the supporters getting to each other, but objects were tossed over the barricade.
However, it does not appear that the trouble escalated into anything serious.
Goal’s Arsenal correspondent Chris Wheatley tweeted: “Few scuffles at the end with some West Ham fans attempting to enter the Arsenal section.
“Stewards did well to prevent further unrest.”
While respected BBC commentator Conor McNamara wrote: “Stewards separating rival fans at The Emirates.
“Objects been thrown. Looks to be under control though.”