Wigan Athletic have launched an official investigation into the unsavoury scenes following Monday night's FA Cup fifth-round clash against Manchester City.
Advertising hoardings were also thrown from the City end of the ground, with many hitting stewards and police.
A statement from Wigan chief executive Jonathan Jackson read: "Whilst we appreciate that the vast majority of supporters who ran on to the pitch did so spontaneously to celebrate a famous victory, we were disappointed with the action of a minority of supporters who acted in an inappropriate manner. Player and staff safety is of paramount importance and we will conduct a full investigation.
"However, it is important to not let the actions of a few supporters detract from an incredible night at the DW Stadium. A special atmosphere was created by both sets of supporters and the match was yet another memorable day in the history of Wigan Athletic."