Your CA sees the same three problems every quarter, and all three are software problems rather than accounting ones.
Invoice numbering gaps
Cancelled bills must stay in the series with a cancelled flag, not disappear.
Missing HSN on line items
Store HSN against the product, not typed per bill.
Place of supply
Interstate versus intrastate decides CGST/SGST against IGST. Let the software decide it from the customer state.
Building something similar?
We will tell you honestly whether a ready product fits or you need a custom build.