The Limited Access permission level is assigned automatically when you provide access to one specific item in a site or subsite with broken inheritance. If the permissions on the specific item are removed, the Limited Access permission level granted previously remains, but is no longer required.
You migrate a site object and notice limited access permissions are not preserved at the destination.
ShareGate Desktop 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.
There is no solution required.