Chairman David Sharpe says Wigan will work with the Football Association and police to review the pitch invasion after their win over Manchester City, reports BBC Sport.
City's Sergio Aguero had an altercation with a fan after the FA Cup tie, and has since claimed he was spat at and sworn at during a post-match confrontation.
Some supporters ripped out advertising boards and threw them towards police.
The FA will study the referee's report and review available footage.
Police say two arrests were made on suspicion of affray following an incident outside the ground.
"Football is a family event and the disruption that players and fans alike faced will not be tolerated," said Greater Manchester police chief superintendent Stuart Ellison.
"As soon as people were on the pitch, we immediately deployed our resources to the front of the stands, where they were able to keep the two groups of supporters apart and prevent any further disruption."