The accumulation of citric acid during fermentation by Aspergillus niger is primarily caused by the inhibition of the TCA cycle enzyme isocitrate dehydrogenase due to a deficiency in manganese (Mn$^{2+}$). This leads to the diversion of intermediates towards citric acid production. The increased expression of citrate synthase, enhanced glycolytic flux, and addition of iron salts may also affect the process, but the primary cause is the disruption of the TCA cycle enzyme.