On Monday afternoon the district issued a fifth notice of violation for excessive visible emissions.
"Valero was preparing for start-up when smoke started coming out of one of the stacks," Roselius said.
A Valero spokeswoman has not returned a request for comment on the district's penalty.
The refinery's first full power loss in 30 years started around 6:30 a.m. Friday. The outage began shortly after crews took one of two transmission lines offline to complete upgrades, said Matt Nauman, a Pacific Gas and Electric spokesman.
Circuit breakers opened after a component of a "protective relay system failed," according to Nauman.
But the San Francisco-based energy company did not directly contact Benicia officials quickly enough about the outage, Mayor Patterson said.
"Why didn't PG&E call the city of Benicia so that we could begin to think about the consequences of power loss to the refinery 15 minutes earlier than we were alerted by Valero?" Patterson asked.
PG&E says it did tell the city, just not as fast as the mayor would have liked.
A company representative contacted the Benicia fire chief and the Solano County of Emergency Services at 8 a.m., according to PG&E spokeswoman Deanna Contreras, adding that utility crews worked quickly and safely to restore power in 18 minutes.
The outage caused gases used in the refining process to build up inside the refinery. To relieve pressure, Valero sent toxic gas to its flares.
Valero, like other refining companies, emphasizes that the flaring process is a safety device.
At first that process sent flames and a huge plume of smoke into the sky, which resulted in the evacuation of an industrial area near Valero and a shelter-in-place order for two elementary schools.
Even that order wasn't clear. Initially, some authorities called for the rest of the city, except for the adjacent industrial area, to stay indoors.
"All other areas of town shelter in place. Keep doors and windows closed. Bring pets inside," said a tweet from the Benicia Police Department.
Minutes later the agency published a corrected tweet, focusing the order on the two schools, but that was not entirely clear.
"No shelter in place for the rest of the (city) except for Matthew Turner and Robert Semple. Everyone's encouraged to close doors and windows," the follow-up tweet read.
On Friday, officials said that only two residents called with respiratory complaints, and there was no indication that anyone was hospitalized.
But, it turns out, the toxic air did send people to the hospital.
Between 10 and 20 people went to the emergency department at Kaiser Permanente's Vallejo Medical Center, according to Kaiser spokeswoman Deniene Erickson.
The flaring continued over the weekend and on Monday as Valero restored operations.
"We may have some intermittent flaring as we continue through safe startup process," said Valero spokeswoman Lillian Riojas in an email Monday.
Meanwhile, the city has begun a top-to-bottom review of its emergency response, according to Benicia Fire Chief Jim Lydon.
"There are some systems that we need to go back and look at and assess their functionality and make sure they're working properly," Lydon said in an interview Monday, adding that he saw complaints from residents about the emergency communication on social media.
After that review is completed, Mayor Patterson is calling for a City Council hearing to explore ways to improve emergency communication.
That hearing would also investigate why Valero does not have a backup power source, something Patterson said she was unaware of until Friday's emergency.
The afternoon of the outage a company official blamed California's greenhouse gas regulations for preventing the creation of an alternative power source.
Valero expanded its refinery in recent years to reduce emissions, according to Don Cuffel, the company's health, safety, environmental director. That expansion increased the facility's electrical load but the company never got a permit to create a "co-generation unit".