Mircea Lucescu played down the missile-throwing but the club are likely to face disciplinary action from UEFA.
The Besiktas coach said: "What is the problem? The fans were just protesting by throwing paper. It's not important and they didn't throw anything serious."
UEFA will examine Frisk's report before deciding whether to take action against Besiktas, who go into the UEFA Cup after coming third in group G. They could be forced to play more games away from Istanbul and Frank Lampard believes they deserve to be punished.
"It turns a bit sour when things are thrown on the pitch and it's just fortunate that nobody got hit," he said. "UEFA have to do something about it. They must have legislation to stop it and have to do something now."
Chelsea will be seeded for Friday's second-round draw in Nyon and will avoid other top seeds such as AC Milan and Real Madrid in the next round.
