Some versions of SharePoint allow you to establish if you want your list view accessible in all folders, only in the top-level folder, or in folders of a specified content type.
When you select a custom view that is not set for all folders in ShareGate's migration tool, there is a chance that the view will not filter your items as expected.
For example, you can select a view set to show only in the top-level folder while navigating subfolders in the migration tool.
If you select that view at the source, the migration tool will filter out all your items based on that view, while you might expect it to only filter items in the top-level folder since that view should only be available at that level.
To avoid issues, you can use the migration tool's default Built-in view or create a new custom view in SharePoint that applies your filters accordingly for all folders.