You are right. I can confirm this. I don't think it's a real bug, more a feature- wish. Perhaps you should report this directly in http://bugzilla.gnome.org/ ?
** Changed in: epiphany-browser (Ubuntu)
Status: Unconfirmed => Confirmed
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Epiphany does not warn when closing a window with multiple tabs
https://launchpad.net/bugs/51658
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