The Iranian club lodged the protest after it arrived 15 minutes behind schedule at Prince Faisal bin Fahd Stadium for training on Friday morning.
Perspolis Football Director Afshin Peyrovani and other representatives of the team urged local officials, as well the Asian Football Confederation to not allow these problems to happen again because this has disrupted their training and recovery schedule.
Peyrovani also protested against the injustice in the allocation of seats for the match.
The Iranian club has sent an official protest letter to the AFC.
Also on Wednesday, players and coaches of Persepolis had to head back home from Tehran Mehrabad Airport after their flight to Saudi Arabia was canceled because the kingdom failed to issue a permit for their flight. The team flew to Saudi Arabia on Thursday evening instead.
Persepolis will face Al Hilal at Prince Faisal bin Fahd Stadium in Riyadh on Saturday evening.