Go into one of the 'some courses'. Turn on editing. Count the number of sections/topics that have content in them.
Look at the course settings for the number of sections/topics to display. Set that to match the number you counted above.
If the courses didn't have that before, then you might have discovered a bug in upgrading ... to report that you'll have to tell the story ... started with what version of Moodle. Process you did to upgrade. etc. It is possible the courses were like that even before you began the upgrade, however, and you might not have noticed?
'spirit of sharing', Ken