Croatia duo Ivan Perisic and Ivan Rakitic blamed their own fans after crowd disruptions allowed the Czech Republic to rescue a draw.
The trouble broke out in the dying minutes of a Euro 2016 game that Croatia were leading 2-1 at the time.
A number of flares and other objects landed on the pitch near riot police, who had been deployed in front of the section housing some very rowdy Croatia fans.
Play was held up for several minutes as the flares and objects were cleared. Croatian fans also started to fight amongst themselves during the hold-up.
Croatia players tried to calm their own supporters in the stands, while an announcement over the public address system at the Stade Geoffroy Guichard pleaded with the fans to “leave the stadium” and not “embarrass” the country.
Play eventually resumed, allowing the Czech Republic to grab a late equaliser after a distracted Croatia conceded a penalty.
Croatia’s players were left very unhappy after the chaotic end to the match.
“I cannot understand why we have to waste out energy to calm our own supporters,” said Perisic, who had put Croatia in the lead.
“We lost our pace when play was suspended because of our supporters,” added Rakitic, who scored their second.
UEFA said disciplinary proceedings would be opened once they had received the official reports from the match delegates and referee Mark Clattenburg.