Thank you for that link, I did read through that and look at the KB article also, but it doesn't actually solve the issue. Making copies of an existing template wasn't applicable to this situation since we want to manage several layouts which may apply to several masterpages which would result in a cartesian number of templates.
To reproduce the problem create a site.master with a panel and inside that a contentplaceholder. Then create a twocolumn.master and specify site.master as its master page and add a contentplaceholder in the content area. Now create a page from twocolumn.master as its master and add a generic control to the content using the add button in Sitefinity. Type hello world in there. If you drag and drop or even click the generic control in classic mode then it will fall out of its content area and emit its text at the footer of the page.
Let me know if you would like source code, however it is easy to reproduce it this way.