Even with pets dogs for instance have to eat a -lot- of chocolate for it to actually hurt them. It's not good for them but it's not cyanide, either.
Really, it's not their similarities to pets that would make human food toxic but the fact that they come from entirely different planets and would therefore have completely different diets and palettes. That's not entirely overlooked since one of the functions of the nanomachines is to digest alien food but I don't think it's specifically brought up anywhere, either, so either some basic diets overlap, lots of people eat bland nutrient-rich pseudofoods when they're in space, or every establishment is really fucking careful about food allergies and such.