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Old244 has a good point -- rusting from the inside-out. Inspect that deep seam inside the trunk where the wheel curve bends down to meet the wheel cut-out edge. It is a common thing for water to travel down toward the front of the car to settle in the corner of the rocker (primarily on wagons where the cargo window seal has failed).

On sedans, water can get into the rocker, but trapped there if debris has acumulated, blocking the drain holes. Peel back the carpet from the door thresholds and open those white plastic plugs to inspect inside.

If the corners of the rocker are rotted out, you'll be able to do a decent salvage job by cutting off the rusted edges of the hole, rivetting a new metal patch over the hole and smoothing body putty over it. Use a good rust stopping paint (Corroless, POR-15, etc.) and correct the cause.