City supporters reported issues with transport to the Ataturk Stadium, on the outskirts of Istanbul, prior to their team's treble-clinching 1-0 win against Inter.
There were also complaints about a lack of toilets and limited access to water at the showpiece final in June 10.
Football Supporters Europe is gathering fan accounts from Istanbul in order to compile a report to present to UEFA.
Ceferin, speaking at the European Football Fans Congress in Manchester on Thursday, insisted this year's final "proved UEFA had learned from past mistakes".
But he added: "We're well aware that in Istanbul not everything was perfect and I'm certainly not playing down the problems encountered by some.
"But let us continue working together to improve what we can improve. I'm thinking in particular of transport links, to better understanding the hosting of disabled supporters and access to water and toilets for everyone.
"I can assure you that next year's Champions League final at Wembley and Euro 2024 in Germany will be a unique experience for fans."
Ceferin also referenced the serious issues endured by Liverpool fans at the 2022 Champions League final against Real Madrid in Paris.
Crushing outside the Stade de France sparked an independent report into the chaos, which found UEFA bore "primary responsibility" for what almost became "a mass fatality catastrophe".
"Given what some of you experience recently, I would understand if I got a cold reception," Ceferin said.
"I also came here to say sorry. We would love to erase events that happened last year. Everyone welcomed the decision to move the Champions League final from St Petersburg to Paris and we know what happened.
"Good intentions are often not enough, we know that and we are sorry for that."
