This issue can occur with the interaction of "Roll Start Time Forwards" setting and two clock events that are close together.
Example Scenario:
Roll Start Time Forwards: Roster - 15mins
Roster Start: 4:30AM
Clock In: 4:25AM
Adjusted Clock In: 4:30AM
Clock Out 4:26AM
In the above example, the system will have rolled the start time of shift to 4:30AM but create a clock off event at 4:26AM which will cause the issue of showing an end time before the start time.