One fallacy that I see frequently in works of popular science -- and also here on LessWrong -- is the belief that we have strong evidence of the way things were in pre-history, particularly when one is giving evidence that we can explain various aspects of our culture, psychology, or personal experience because we evolved in a certain way. Moreover, it is held implicit that because we have this 'strong evidence', it must be relevant to the topic at hand. While it is true that the environment did effect our evolution and thus the way we are today, evolution and anthropology of pre-historic societies is emphasized to a much greater extent than rational thought would indicate is appropriate. 

As a matter of course, you should remember these points whenever you hear a claim about prehistory:

• Most of what we know (or guess) is based on less data than you would expect, and the publish or perish mentality is alive and well in the field of anthropology.

• Most of the information is limited and technical, which means that anyone writing for a popular audience will have strong motivation to generalize and simplify.

• It has been found time and time again that for any statement that we can make about human culture and behavior that there is (or was) a society somewhere that will serve as a counterexample. 

• Very rarely do anthropologists or members of related fields have finely tuned critical thinking skills or a strong background on the philosophy of science, and are highly motivated to come up with interpretations of results that match their previous theories and expectations. 

Results that you should have reasonable levels of confidence in should be framed in generalities, not absolutes. E.g., "The great majority of human cultures that we have observed have distinct and strong religious traditions", and not "humans evolved to have religion". It may be true that we have areas in our brain that evolved not only 'consistent with holding religion', but actually evolved 'specifically for the purpose of experiencing religion'... but it would be very hard to prove this second statement, and anyone who makes it should be highly suspect. 

Perhaps more importantly, these statements are almost always a red herring. It may make you feel better that humans evolved to be violent, to fit in with the tribe, to eat meat, to be spiritual, to die at the age of thirty.... But rarely do we see these claims in a context where the stated purpose is to make you feel better. Instead they are couched in language indicating that they are making a normative statement -- that this is the way things in some way should be. (This is specifically the argumentum ad antiquitatem or appeal to tradition, and should not be confused with the historical fallacy, but it is certainly a fallacy). 

It is fine to identify, for example, that your fear of flying has a evolutionary basis. However, it is foolish to therefore refuse to fly because it is unnatural, or to undertake gene therapy to correct the fear. Whether or not the explanation is valid, it is not meaningful. 

Obviously, this doesn't mean that we shouldn't study evolution or the effects evolution has on behavior. However, any time you hear someone refer to this information in order to support any argument outside the fields of biology or anthropology, you should look carefully at why they are taking the time to distract you from the practical implications of the matter under discussion.