This isn't a bug. As Dave points out, gnome-terminal runs as a single
process (to do otherwise would make it very difficult to do things like
move tabs between windows etc).
xkill works by finding which PID a window belongs to and killing that.
Hence, running it on a single terminal window will kill all instances.
The same is also true for other applications, eg nautilus and gedit
** Changed in: gnome-terminal (Ubuntu)
Status: New => Invalid
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xkill kills all gnome-terminal instances
https://bugs.launchpad.net/bugs/609089
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