The complaint was filed on Thursday by 32 people unable to travel out of Bangkok as a result of the financial wrangle between the airline and its Korean agent Skyjet, and by nine tour operators who sold Seoul travel packages to them.
The group asked police to act as a mediator between them and the airline in seeking financial compensation.
PC Air's flight back to Bangkok from Incheon International Airport was cancelled just before takeoff on Wednesday as a result of the financial wrangle. The airline's sole aircraft, an Airbus 310-222 with 200 seats, was refused clearance from Incheon International Airport pending settlement of aircraft service fees including refuelling costs.
The plane was grounded for just over 25 hours, leaving about 400 passengers, mostly Thais, stranded at the South Korean airport.
The plane was eventually allowed to take off and arrived Don Mueang airport at 4.30am on Thursday, with a total of 218 Thai passengers, mostly members of tour groups to South Korea.
PC Air managed to get permission to take off after settling the amount owed which included ground-handling charges.
Angry passengers who returned to Bangkok in the morning have also filed complaints.
"I'm sorry for what happened," said Peter Chan, PC Air president. "We are trying to get all the passengers back home as soon as possible."
The plane was only allowed to leave after the airline paid its fuel bill in Seoul, said a PC Air official who asked to remain anonymous. "There seems to have been some misunderstanding caused by our broker in Seoul," he said.
A Bangkok-based passenger, who declined to disclose his name, said he was scheduled to leave for Seoul on a PC Air flight from Don Mueang on Wednesday night, but had to return home after he was told the company’s sole aircraft was impounded at Incheon.
Tour operators had to find accommodation for their customers who live in other provinces, he said.
CSD deputy commander Pol Col Akkaradej Pimolsri said he had directed investigators to question the petitioners and ask PC Air to send a representatives to discuss a settlement with its clients.
During the talks with police, the tour operators announced they would refund travel costs for the 32 people who missed their flight to Seoul and wanted to cancel their trip.
Those wanting to continue their holiday plans with PC Air would have to postpone their journey and leave Bangkok after Nov 3.
The operators offered to find seats on other airlines for those who still wanted to visit South Korea but did not want to fly with PC Air.
Nine of the 32 people have decided to cancel their trip and asked for a refund.