This was a error on my part but let me explain.
When I do a upgrade to my site I delete everything in the manager as well as in assets/snippets. But it was late and I accidentally deleted config.inc.php in the manager. So I decided to grab a config.inc.php from another site and change the database login. But what I forgot is to change the table prefix. The table prefix was the name from the other site. So I went ahead and did the upgrade. So during the upgrade process the installer didn’t tell me that so and so prefix was not found. So i did the upgrade and the installer created the exact same tables as you would do a normal fresh install. I think there should be a warning saying the table prefix wasn’t found.
As I say its more of a HUMAN error. But sometimes working late and I am sure we have all been there these little extra error checking would be nice.