Current we dont have feature to add the reason code while scanning items for any stores this will lead to fraud in future.
In Ax we have an option reason code for counting journal.
We have an option for discounts/price overrides it can be recorded in transactions.

Repro steps:
1. Open MPOS
2. Select Stock Count
3. Choose NEW
4. Now it should ask for Reason Code to capture the reason
5. Data must be transmitted into D365
Ideas Administrator

The improved stock count operation in POS allows the user to add custom notes for counting journal or specific counting lines, which after HQ processing, are attached to corresponding counting journals. You might want to leverage this function to capture reason codes. - Boyce Zhu, Principal Product Manager for Dynamics 365 Commerce