Symptoms
You migrate a site object and notice limited access permissions are not preserved at the destination.
Details
the ShareGate migration tool does not migrate the Limited Access permissions. When you migrate an item with custom permissions (disabled inheritance), the Limited Access permission is added to the site hierarchy automatically by SharePoint.
If an item had his permission inheritance restored over time in the source, the Limited Access permissions that remain are useless and their removal will not affect the users' access to their content.
Solution
There is no solution required.