As you can see from the comments mdsumner and agstudy were able to answer why this is happening, though agstudy was unable to recreate it with the dataset available. I did find a work-around for this problem.
library(rgdal)
library(rgeos)
library(ggplot2)
#LOADING IN DATA
africa = readOGR("directory", layer="filename")
#FIXING THE NON-NODED INTERSECTS#
africa = gBuffer(africa, width=0, byid=TRUE)
africa.map = fortify(africa, region="ID")