Hi Srii
It is Standard SAP Functionality. But as per adjustment It will net off while taking the excise credit. If you feel wrong you make a Journal Entry as follows:
Output Basic + Cess + Hscess is Debit
Input Basic + Cess + Hscess is Crdit
Incoming clearing Debit
Outgoing clearing Credit.
Check the your accounts team before made this entry.
With Regards
Balaji Sampath