I cannot reproduce this problem on OS X El Capitan 10.11.1 with Oracle Java 1.8.0_60 for yEd 3.14.4. My test case was as follows:
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Create two normal nodes.
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Select both nodes and use CMD+ALT+G to group those nodes.
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Double-click the group node to navigate to its inner diagram.
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Select the first normal node and use CMD+C to copy said node.
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Use the "Back to previous view" button in the tool bar to navigate back to the parent diagram.
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Create a third normal node, select it, and use CMD+ALT+G to create a group node for the latest normal node.
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Double-click the second node to navigate to its inner diagram.
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Use CMD+V to paste the previously copied normal node.
Additionally, I also tried the same approach with using CMD+DOWN and CMD+UP for navigating into and out of groups (instead of using mouse and tool bar as described above). Everything worked as intended for me.
So, either your workflow is distinctly different from mine (in which case a step-by-step explaination or a screen cast would be great) or this is something specific to your machine.