Friday night's game, which ended 1-1 on the pitch, was a 'difficult fixture' for police officers, according to Mark Lawrie, from British Transport Police (BTP).
The superintendent for operations and crime in London and the South East said: "A lot of rivalry between these two and unfortunately it turned into missiles and flares being thrown at BTP Ops Support Unit, BTP Sussex and Sussex Police."
Supt Lawrie said, 'importantly', no officers were injured and arrests have since been made, adding: "Thank you to the proper fans."
PC Darren Balkham, who serves as a police liaison officer to Brighton and Hove Albion and its supporters, wrote on Twitter: "Firstly thank you for those who attended the game tonight.
"I am aware of some issues that occurred in the north stand area on egress. We will sit down with the club review CCTV and look to see what the cause was."
The club also issued a statement on Saturday afternoon (January 15).
It read: "The club is aware of the congestion and delays encountered by a number of supporters leaving the north east corner of the stadium after Friday’s match against Crystal Palace.
"We wish to apologise for any inconvenience caused, and to thank fans for their patience.
"Working with the police, the club’s operations staff were monitoring the congestion on CCTV monitors from the stadium control room at all times, and were able to direct staff and police on the ground to ease the congestion as quickly and as safely as possible.
"When special stadium egress measures such as those for Friday's game are implemented, staff must manage an ever-changing and dynamic situation. As usual, all plans will be reviewed and, where necessary, refined for future matches."