West Ham face crowd charges
League One Millwall were cleared of any charges.
The FA said in a statement its independent regulatory commission found West Ham failed to ensure their fans refrained from violent, threatening, obscene and provocative behaviour.
The club had also failed to keep its supporters off the field of play.
"The Commission will reconvene on Friday 15 January to consider the issue of sanctions," the statement added.
West Ham were originally charged on four counts of failing to control their fans while Millwall had faced three charges.
West Ham's 3-1 extra-time win over their east London rivals on Aug. 25 was marred by crowd violence before kick-off and during the match.
Supporters invaded the pitch twice after West Ham scored and a 44-year-old man was taken to hospital with a stab wound.