If you navigate to:

onRecord > Procedures > Schedule> Master Schedule 
Filter for Group Type: Advisory, Academics etc > School Level> Section Name (such as Homeroom- Teacher Name for example)

On the Date you are seeing the issue, hover over the Edit link and you will see "Single Section One Day" which is an indicator that a meeting time was added manually for this section. If you click on the Edit link you will see two meeting times. The one originally scheduled (for example 10:20am-10:55am) and the one that was manually added (11:15am-11:45am). Cancel the manually created meeting time.