Cloner doesn't assign categories correctly

When cloning sites in my network, categories aren't assigned to posts correctly. Since then I updated a copy of the site and tried cloning after disabling all of the other plugins (except WMPUdev network activated plugins) and I get the same results, this also seems to impact the menu which includes categories and slightly varies in the clone. Also, I switched to "twenty twelve" which is one of the default WP themes

Debug.log is saving some database errors that seems to be related.