Here we see some notable patterns of controversy. Egypt (which hosts three out of the top-five most controversial articles on the continent) and North Africa have a lot of contentious articles. So too does the Horn of Africa (more than heavily populated parts of West Africa).
Some of the most controversial articles (e.g. the Great Pyramid of Giza) seem to rise to the top of the list simply because there is a lot written about them and the Wikipedia article then becomes a site for discussion and conflict. But in other places/cases, we see more violent, material, and political conflicts spilling over onto the talk pages of articles (e.g. the Somaliland article).
It is interesting to point out the average controversy score on the continent (96) is quite similar to the average in the British Isles (110). In other words, in both places, most articles simply aren't controversial at all and we see a pronounced long-tail effect with only a few articles subject to the brunt of argument and conflict.
But, we do see a lot more total conflict in the British Isles. Given that there are also far more articles about the British Isles than all of Africa combined, the higher total amount of controversy is simply a reflection of the increased amount of human labour and attention focused on the region.