I agree with Ron here:
If you trust the accuracy of the calculations, you must do something about it, not necessarily because of the NEC, because that would effect you only if doing new modifications/work to that equipment, but for liability now that you know.
The only Assumptions are: did they calculate with a known available fault current at the primary or was the study performed with "Infinate" fault current available?
That is what I would ask. The rest should be just plugging in the numbers of conductors, length of conductors,pairs per phase and magnetic or non-magnetic conduit.
If after you have these questions answered (because you really can question the study) and found it to be true, think about series rating:
http://cooperbussmann.com/2/SeriesRatings.html
to protect your existing installation, however maybe think about adding a UL listed combination of high current limitation in front of those breakers, that by themselves are exceeding the existing available fault current, could be your cheaper fix.
Just my $.02
edited to correct my poor spelling.