By default, the system will attempt to schedule a course for the same block/teacher/room through all terms of the course. However, if a course with a higher priority, a single section, etc would cause a conflict, the system will adapt and may place the course in a different block in a later term.

You can affect the course priority of a course within its course settings by:
  1. Navigate to Academics > Scheduling > Requests and schedules > Departments & Courses
  2. Select the edit/pencil icon to the right of the course
  3. Select the Schedule tab for the course
  4. Check the 'Course Priority' dropdown at the top
Additional Course Priorities can be defined under Core > Settings > Table Values> Course Priority.

If using snapshots (highly recommended), you may also try restoring to the point before the mismatched blocks occurred, and attempt other options within the 'Generate Master Schedule' button/settings, as here:
GMS_Options 1GMS_Options 2

Additionally, as an example, if a teacher or room conflict may be causing the conflict, you can also choose to schedule only blocks on your first run, and then run the other options in a second/later run (again, from the 'Generate Master Schedule' button):
Schedule Maker: Information to Schedule