A glitch in Japan Airlines Co.’s check-in system caused delays in departures Wednesday at Tokyo and other domestic airports in Japan, the company said. Customers also experienced problems on the airline’s website when trying to make reservations for domestic flights and when checking in for international flights. At Tokyo’s Haneda airport, one flight was delayed by an hour as staff worked manually to complete the check-in process for passengers. The problem was detected around 4:30 a.m. on Wednesday and JAL is working to restore the system and find the cause of the glitch, according to the com…