Items can become orphaned when the course you are copying into has less sections than the course you are taking content from.
You will be able to see orphaned items when you have editing turned on but not when when editing is turned off, students cannot see orphaned content.
Follow the instructions below to resolve this issue:
1. With editing enabled.
2. Scroll to the bottom of the Moodle page until you see the Add section button.
3. Repeat until all of your content is in a section.