The most common reason is that the leave type is not configured to deduct from an allowance.
To check this, go to the Settings > Leave Types page and click on the leave type which is not deducting.
The DEDUCT FROM ALLOWANCE dropdown controls whether leave types deduct from allowances.
- If this is blank then requests of this leave type will not deduct from an allowance.
- If you wish it to deduct then select which allowance to deduct from.