It is difficult to tell if the 'holes' you see are one or two squares. There are also other anomalies ... seperately, to the southeast of Djenne and to the southeast of Timbuktu the border seems to extend farther than it should.
Its possible cities are not the only source of border 'pushing' ... the new resource buildings might have an effect. While programming that stuff, Firaxis may have made border generation other complexities.
There is something interesting to note here ... there appear to be two workers by Djenne ... do workers have hit points now? Or perhaps its two workers joined up that, in Civ3, would have just been a stack of workers.