Honestly, his big mistake was not turning on said former comrade with more vigor. Sankara was too kind and too sentimental to be a strongman - perhaps that's part of the reason why his administration was so fantastic, but also part of the reason why it fell.

France was constantly trying to undermine him (including by supporting said former comrade against Sankara), though his own lack of diplomatic tact didn't help matters. He certainly preferred a revolutionary's language to a diplomat's.