The Whites won 2-0 at Wham Stadium thanks to goals from Elias Kachunga and Aaron Morley to clinch a Wembley final against League One rivals Plymouth.
Bolton supporters invaded the pitch after the final whistle, and there were also complaints from away fans purchasing tickets in the home zones.
Stanley says they will now meet with the relevant authorities to discuss how to avoid similar incidents in the future.
An official statement read: “Following the incidents at the end of Wednesday night’s semi-final, the club agreed to meet with the relevant authorities, including the police and the EFL, to discuss what processes are required to avoid similar problems in the future. . .
“The investigation will also focus on how a minority of Bolton Wanderers supporters managed to gain access to tickets for the home sections of the stadium.
“We will make an additional statement at the conclusion of the investigation.”
Accrington boss John Coleman also shared an update on midfielder Liam Coyle, who was stretchered off after a collision with James Trafford.
Coyle suffered “multiple facial fractures” and will be monitored by the club’s medical staff in the coming days.
Trafford was booked after the incident, but Coleman felt the Manchester City loan man was lucky to stay on the pitch.
Speaking after the game, Los Blancos manager Ian Evatt said: “I didn’t think there was anything to it. I thought it was a tough yellow card to be honest.
“He has won head first and it’s just a horrible clash of heads. I really hope Coyle is doing well and on the mend.
“It was a nasty crash and it is very important that he maintain his health. Let’s cross our fingers for him.”
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