There are many reasons for this. In the past the division of borders did not respect local nations, so in some countries enemy nations were grouped together, local leaders for whatever reason might have instigated these differences instead of working on them, there is the case of the Rwanda Genocide in 1994 where the government majoritarily composed of Hutu promoted the massacre of the Tutsi. Also there are economic considerations, land means potential control over minerals and oil, for instance South Sudan retains 75% of the former Sudan's oil reservation, in Angola there were bloody conflict between the government which took care of the oil and the rebels who controled the diamond mines. It is also possible to add religious conflicts, mainly Muslims versus Christian over the continent.