When I took mine apart and when I got the SC2 Hybrid kit, I noticed that the included thermal pads were a bit weird even for stock ones in that they used a very sticky adhesive on both sides. Even without running the card this stuff gets left all over anything it touches for any amount of time - so all over the PCB, all over the backplate, fans, VRAM, VRMs, yeah. I could see how a bad few pads or getting too hot too quickly might cause this - there's a 1.5mm thick pad right under that EVGA logo.
They're super cheap and really bad. I read somewhere they're something like 1W/m.K conductivity, which is around the lowest you can get but it's completely normal to get that as stock on everything. What makes them super cheap and really bad is the adhesive. If you compare them to the Fujipoly ones you get with a Bitspower block, or the EKWB ones, which are only adhesive on one side and use a tacky adhesive rather than the liquidy one you get with these cards, the difference is amazing. Even the ones you get on Gigabyte cards are far better - same green 1W/m.k pads, different adhesive.
I saw these and was pretty disappointed. I'm not an electrical engineer, but from everything I've seen over the years and just common sense, the pads that go in these should be single sided tacky and the tacky side needs to be placed onto the backplate and heatsink - not onto the PCB. Again, not an electrical engineer, but first port of call was to order some halfway decent ones to replace them.