You may re-try the operation, and you may need to clean up the half-created data first before re-creating.

I encountered this "fantastic" error when I tried to create a new variation in my site. I did that in many other occasions without problems but today it has failed. The result is that the process makes a partial copy of the root variation. I don't know the reason, but I have encountered the causes. It failed when the variation process tried to copy two pages to the destination site. The solution was to delete the two pages that cause the error.

To discover what page are causing the problem you can trace de Content Data Base of your site during the create hierarchies process. You will see that the variation process throws an SQLException due a violation of Primary Key on a table. This is the error that I saw in my event viewer and in the trace: Violation of PRIMARY KEY constraint 'PK__#ExportObjects____56256D26'. Cannot insert duplicate key in object 'dbo.#ExportObjects'.  The statement has been terminated.  If you save the trace in a table and launch a query like this SELECT * FROM MyStoredTrace WHERE TextData like '%name_of_origina_variant%' ORDER BY starttime it will return a lot of rows. To know what is the problematic page search the last processed page.

Another way to discover it is to review the site generated and determine what the first missing page is. It Is probable that this page produces an error when you try to move or copy.