This is entirely speculation but the fact that there are active wars in the continent might affect how the data is classified. I don’t know how the article you posted defines homicide. There are some rules here https://www.unodc.org/unodc/en/data-and-analysis/statistics/iccs.html and it seems that deaths during war conflicts might not be counted as intentional homicides. Latin America hasn’t had many wars but had/has many conflicts involving guerrillas, cartels and political groups. Is it possible that many of the resulting deaths are counted as homicides whereas similar violence in Africa is counted as, for example, civil war deaths?