Symptoms
When migrating files into a OneNote folder, you see this message:
The OneNote Notebook '{0}' contains files that will not be visible within the notebook. Those files may only be visible from the explorer view at the destination.
Details
This warning message occurs when you migrate a file into a OneNote folder that is not associated with OneNote (OneNote files have .one or .onetoc2 extension).
Since clicking a OneNote folder opens the OneNote online editor, the file that is not associated to OneNote will not be visible in the notebook. The only way you will be able to see or access the file is using the Explorer in Sharegate.
Solution
The best solution is to migrate the files that have extensions which are not .one or .onetoc2 out of the OneNote folder, and into another folder within a document library that is visible to you.