Since toll takers were removed back in March, drivers have to pay with FasTrak or they will get a bill in the mail.
But so many people were mailing in payments that workers couldn't keep up.
Hundreds of drivers were charged late fees for payments that were never processed.
Drivers had the option to pay by phone but, the wait times have been long and the related website has crashed a number of times.
The Metropolitan Transportation Commission says more people have been hired to deal with the demand.