Please check as follows to allow proration in your pay element correctly:
Go to the Payroll module and click Pay Element Setup.
Select the Pay Element ID and click the three-dotted button.
Ensure to select Prorate by Hire Date, Prorate by Cessation Date, and Prorate by NPL in the selected panel (select the properties from the left panel and arrow over to the right if not selected).
Go to Setup and click Pay Group Setup.
Click Leave Cut-Off Date and ensure the NPL cut-off is selected correctly.