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Create two packages (package0 and package1). Drag and drop package0 from the model explorer in package1 on the diagram. package0 will appear as contained by package1 while the model shows two independent packages. This problem occurs for other elements such as datatype, class, ...
Created attachment 171618 [details] Inconsitency between graphical representation and actual model information
It is not really a bug. It is just confusing and may lead to incorrect inferences. I think QualifiedName should be automatically displayed for all the elements graphically represented out of their namespace. At least, this should be customizable in preferences.
Several bug are open related to the ContainmentLink behavior -> see Bug318000 *** This bug has been marked as a duplicate of bug 318000 ***