I run into this twice already and I figured it will be best to inform you so you can investigate if someone else had that kind of issue.
When running cloner on my multisite environement - I end up with content deleted from my taxonomy terms table - no clue whatsoever why but when cloning there is an output - error copying menus - wrong id and the cloning goes on.
Is there a cloning log that I can send you to investigate ?
Thanks for great plugins that you guys provide I really like them.
For now I dealt with the issue by going back in snapshot and recovering the missing tables but I guess that there is more to that and it needs to be investigated further.