it's obviously not a good thing to eat loads of moldy food. The mycotoxins (such as aflatoxins) seem to damage the liver.
But I can't believe our ancestors always had flawless foodstuff. Or maybe some of the stored reserves got a bit moldy. Shouldn't our body have developed machanisms against those mycotoxins? Or maybe the mold strains on paleo food do not produce such strong poisons? After all, there's no risk in drinking wine, as those yeasts do not produce any toxins.
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The worst mycotoxins (aflotoxins, ergot alkaloids, etc) are produced by molds that occur on stored grains and legumes. There hasn't been enough time to evolve resistance - these haven't been a substantial part of the human diet for any more than 10,000 years tops.
Added: Some more answers to your question can be found in this paper http://toxicology.usu.edu/endnote/329c6ba9a2d273760688e0d%26ie.pdf Especially check the subsection headed "There is limited protection from co-evolution".
Our ancestors were probably in the habit of eating their food fresh, not storing it. Especially if they were traveling light. So I assume the food wouldn't have had a chance to get moldy. If it did, I bet they'd throw it out like we did, or eat around it.