Considering the general practise, books of accounts are not maintained to provide separate heads of ITC as per requirement of Table 14 of Form GSTR-9C. Hence, it is likely that your CA has provided combined figure of entire ITC against A (Purchases), which is generally main-head (among listed heads in said Table 14) for majority of ITC for most of business/es.
And, this I believe same is quite wide-spread practice followed by business/es & CAs across the board.
Once there is no allegation of any fraud or malafide intents etc, reporting ITC in such clubbed manner should not have any serious adverse consequences under GST law/s. This is more so when figures of ITC reported in Form GSTR-9 is not in question.
Furthermore, there is no procedure prescribed to correct Form GSTR-9C once filled.
It should explain 'the practical difficulties' arising from method of maintaining books of accounts to Dept's officer.
At the maximum, he may propose general penalty u/s 125 of the CGST Act, 2017 and same should defended by you using Section 126.
These are ex facie views of mine and the same should not be construed as professional advice / suggestion.