Seems our modern obsession with clean pure foodstuffs has once again bit us in the backside. In this case, it's "ultra-filtering" of honey to remove those cursed unnatural pollen particles. This allows sugar water to masquerade as honey.
Of course, this example isn't very paleo, being so glycemic. Does anyone have examples that are more paleo?
Please confine your answers to those cases which are motivated by hygienic muddle-headedness, like this one.
I think just about everyone in the natural/alternative and/or Paleo communities is familiar with the issue mentioned by Nance, as well as the various synthetic -ides used on all non-organic produce. Probably the most fundamental alteration of our nutrient sources in the name of hygiene or sanitation is the chlorination (i.e. poisoning) of virtually all urban and suburban water.
You don't have to be paranoid about every food you buy because of this, but if you buy foods that are not local or organic, I recommend checking if they have been irradiated, as the FDA requires them to be labeled as such. See the above article for the irradiation symbol.