Where you've set an element type as a Regular Payment, the dates won't be contiguous, meaning it's not pro rata.
The costs for regular payments apply at the end of the financial week (usually a Sunday, but not always), and you'll see that the start and end dates of the costs align with that day.
If you've got a pro rata element with gaps in the costs, please log a new case including the following:
Ensure you’ve got the IDs for examples.
Screenshots of the following:
Cost screen.
Rate configuration.
Element type configuration.