Some reported waiting in line for over an hour.
The long waits were due in part to increased security measures at the gates, including handheld metal detectors and extensive bag searches for every attendee.
But fans blamed the long lines on a lack of adequate personnel and number of open gates.
"I'm up for security, it's a great thing, but this is obnoxious," said Craig Gilles.
Stadium security officers would not discuss the long waits, but did say the big reason for the frustration was due to ticketholders waiting until the last minute to enter the stadium.
"It's not OK, it's not OK. Holiday Bowl has to do better," said Mary Tael and friend Helen Cortez, who say they waited an hour to get inside.
After waiting, some fans rushed the gates, further adding to the chaos.
Extra security at Qualcomm for Holiday Bowl translates into horrible waits to get inside. Fans R livid. Fox5 at 10PM pic.twitter.com/gRBCxCYdz9
— Salvador (@SalvadorSDnews) December 31, 2015