Sharegate displays the following error when trying to open a site collection or a site:

The requested list or document library cannot be found. It may have been deleted.

This error often happens when a list or document library that was corrupted, got deleted and now resides in the recycle bin. This makes SharePoint react abnormally which reflects in Sharegate. You can confirm this by using SharePoint Designer. Connect to your site collection and click on Lists and Libraries. If your lists and libraries don't appear as they should, that confirms that this is the issue.

To fix this issue, the problematic list or document library will have to be deleted permanently. To do this, go to the Site Settings of the problematic site collection and click on Recycle Bin. Delete your lists and document libraries from the Recycle Bin. They will also have to be deleted from the second stage Recycle Bin. To do this, click on Deleted from end user Recycle Bin and delete your list and libraries.