This is by design, so that any exceptions to the schedule have to be approved. If you schedule an employee to work from 9-5 and they leave at 5:30, the timecard will show they worked until 5:30, but only pay them until 5. You decide to extend it.
However, you can have the system automatically do it. In the
Manage My Business » General » Manage My Payroll, Shifts and Labour Rules
You can turn allow the system to pay them to the next 15 minutes by selecting the below option. This will round the employees PAID timecard to the next fifteen minute increment when they are checking in/out XX minutes.