FWIW, this is the typical input structure. As you can see, when the pin is pulled up, but VDD = 0, there's potential for current to flow. How much, depends on your external pullup. Whether that's causing your issue, I can't say, but I'd have my suspicions.
i will certainly address this regardless, but, and its a big but. The damaged pins seem to be A0 in both cases, yet the pin with voltage on it is D12. Perhaps they are in somewhat multiplexed inside the chip ?
Either way, this is the most likely candidate for now
that is a possibility, one which i considered when adding the external pullups, I am going to go over the original schematic, and the actual connections and make sure they tally up ok, then I will post a schematic here to see if anyone can spot something I may have missed. (or am ignorant about)