Depends on where Mission Bay. There is an intersection of Class B boundaries right over the VOR. To the south is the SAN surface, but to the north are 1800' and 4800' floors. And that's assuming no Class B clearance.
Besides, if, as stated, they received a Notice of Proposed Certificate Action, it specified exactly which reg(s) the FAA claims was violated. and how they were violated. For illustration, this is a sample content of a simple NPCA claiming a common IFR altitude violation. (yes, from a real case). Point is, a claimed violation of the minimum altitude rules will cite the minimum altitude regs; a claimed violation of Class B will cite the regulation requiring a Class B clearance.
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