The problem is that the native peoples have a lot of history of interacting with each other in the form of wars and genocides. In Africa, national independence wasn't really national in the sense of the European countries. A close analogue would be Yugoslavia, where warring kingdoms were forced into a single country. Independence condemned African minorities to rule by figures from neighboring tribes or kingdoms that had previously massacred them before the advent of European rule. This was the real tragedy of decolonization - it placed oppressed peoples under the rule of their oppressors simply because they had been administered as a single geographical unit/province under European rule. The independent countries were simply empires covering many (pre-European rule) kingdoms, but without the (relative) impartiality of foreign rule. This is the source of many of the internal genocides and civil wars in former European colonies.