The combined fines totaled $42,100.
The report is one of handful of investigations into the deadly blaze. The official cause of the fire has not been released. However, officials have said it started in a loading dock area where employees said they smoked cigarettes.
The state's safety report cited the department for four violations, including one "willful" violation for having an inadequate command structure that could ensure firefighter safety in an emergency. In all, the department was hit with four violations totaling $9,325 in fines.
City officials did not immediately respond to a request for comment.
Last month, a city-appointed panel reviewing the Charleston Fire Department made 20 recommendations, including improving leadership command at fire as well as hiring other top firefighting officials.
Among the fines issued Thursday were two for firefighters on the scene not wearing full protective gear: air tanks and body protection.
The store was cited for a "willful" violation for having padlocked doors. It was also cited for fire doors that did not work and not having an emergency action plan in place for its employees.
One store worker was trapped during the blaze but was pulled to safety by firefighters.
Store owner Herb Goldstein defended having the doors locked.
"Our managers locked the doors at closing time to keep criminals and transients out of the building, and only when there were no customers present," Goldstein said in a statement.
The store was fined $32,775 for three violations.
Written by Associated Press