I've said it before, you want a totally guaranteed rust free MN12, you want a native car from the south west, but not so far west that it's near the Pacific. Humidity and Rain water alone can do this much damage, and it probably didn't help that car had ground effects for probably 25 years, sadly this is what I expected when you were asking about pulling them. I'm not saying they cause it, but it gets horribly out of control under them after it starts for some reason. I've never seen a base/Sport/LX rockers as badly rotted out as SCs up here.
I'm with you, my pride and joy cougar just developed a spot on the rear right rocker. It's still pretty small, but it was extremely disappointing nonetheless.
However, it was driven through several winters, and that's the only spot on the car with significant rust (I've been under several times with a fine tooth comb and have yet to spot any other trouble areas). What sucks even more is that the original paint is in great shape.
What's funny is that if you look up the type of foam they pump into chassis cavities, it's not supposed to absorb moisture. Yet, here we are.
Maybe you could take the fender off and see exactly how much rust is in that area? Try scraping some of it off or tapping it with a screwdriver to see how deep it is.
I'll be making a post detailing my repair on my rocker soon, once I get the guts to dig in. Professional repair is way out of the question for me, but I can't just watch it get bigger.
Even if the foam didn't absorb moisture it still creates crevices and gaps for the water that inevitably gets in to pool up and create "hot spots". The rear of the rockers are especially prone to it since the foam was injected through the frame rail holes, towards the front, and these holes are exposed all the way from the rails to the outer rockers, right in front of the rear tires. The sunroof drains into them too if you have one. Simply put the rockers on these were/are ticking time bombs. Ford somewhat lessened the severity in 93 when they switched from selective galvanization of sheetmetal to full, but they never stopped stuffing them with foam and using inadequate drains.
That's another thing! There are drain holes punched into the backs of the rockers along the bottoms. If no one has noticed it's understandable, they're TINY go ahead and look for them some time(if they're still there lol). They're maybe 1/16" tall, 1/8" wide, in a half moon shape, so they can clog very easily, including on undercoating and "rustproofing" methods such as Ziebart, where they liberally apply a thick clumpy coating at random inside the panels with a wand, plugging those holes from the inside and leaving even more random low spots and crevices for the moisture that still gets in to stay.