The biggest complication is that the current notion of human race is largely based on skin color (with a few adjacent physical traits), which has very little to do with population genetics. In particular, black skin color is a dominant genetic trait, meaning that you can easily have individuals and even entire subpopulations that are black skinned, but have much more genetic similarity to traditionally white skinned populations (being descendents of a few black skinned individuals who married into a larger white skinned population) - while they would still be categorized as "black" in terms of race. Conversely, genetically isolated black skinned populations are also often lumped together as "the black race".

Another major complexity is that some races are defined more by genealogic ancestry than by genetic ancestry or easily identifiable physical characteristics. For example, people are normally considered Jewish if they have a Jewish mother. This leads to many genetically disparate subpopulations being lumped together as a Jewish race.