Levski played most of the last-16 game with 10 men after Moroccan defender Youssef Rabeh was sent off for a robust tackle in the 14th minute.
Levski substitute Hristo Yovov was also shown a red card by referee Stanislav Stavrov in the first half for invading the pitch to protest against a disallowed goal.
Levski coach Georgi Ivanov was dismissed during halftime and police had to keep him away from Stavrov, the latest in a string of disciplinary problems which have marred Ivanov's coaching career.
"It's ridiculous," said Ivanov, who was sent off for the second time in less than three weeks. "It's a pity. I'm afraid that the championship will not finish in the spring if they (referees) continue officiating like this."
Levski's fan club said in a statement later that fans would be gathering in downtown Sofia on Monday to protest against the Bulgarian Football Union (BFU) and the referees.
