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When I run xkill in terminal a X (cross sign) appears which seems to kill that GUI process (application) on which it is hovered and clicked. I expect the same behavior for GNOME Terminal (since in my understanding it is also a GUI application). But I get different behaviors under different display manager.

Under x11: enter image description here

Under Wayland: enter image description here

It seems xkill can't kill terminal in Wayland.

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    Note that Wayland is not a display manager but rather a display server protocol, which is a rather big difference. X server software like xkill does very well work in (supposedly all) different X display managers, but naturally not in Wayland ones – and the other way around. – dessert Jan 20 at 12:11
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    You should see the same behaviour with other GNOME applications (ones running in Wayland instead of running under the XWayland compatibility layer), e.g. Files, Documents etc. – pomsky Jan 20 at 13:45
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    @pomsky Is there anyway I can determine which application is running under which layer? – Kulfy Jan 20 at 14:27
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    "Is there anyway I can determine which application is running under which layer?" is a good question. Maybe worth a separate question thread at AskUbuntu :-) – sudodus Jan 20 at 14:52
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    @sudodus Yeah. But I think I should read more about Wayland. I'll try to have a self-answered Q&A later on. – Kulfy Jan 20 at 16:44
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According to a bug report and response by Jean-Batiste Lallement:

This is a known issue with wayland documented upstream on https://fedoraproject.org/wiki/How_to_debug_Wayland_problems#Many_well-known_X11_utilities_don.27t_work

Don't hesitate to file any bug you may find.

To quote Fedora documentation:

Power users are familiar with a large range of X11-related utilities, like xkill, xrandr, xdotool, xsel. These tools won’t work under Wayland session, or will only work with XWayland applications but not Wayland applications. Some tools might have a replacement which allows to perform similar tasks.

Thus, it's a well known issue. You may want to submit a bug report (and probably it will be marked a duplicate) or wait until upstream fixes things.

For the time being, you may want to stick with the pkill or kill in terminal

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    I believe this isn't a bug but it is supposed to be like that. – Kulfy Jan 20 at 14:30
  • @Kulfy: Why do you think I don't use Wayland? – Joshua Jan 20 at 20:28
  • @Kulfy This may not be a bug in the sense of software being broken, but it is a bug in the sense that Wayland promises maintaining backward compatibility with X11 applications. – Sergiy Kolodyazhnyy Jan 20 at 20:53
  • @SergiyKolodyazhnyy Then why I was able to kill nautilus in Wayland by clicking on desktop? Is it because it was running under XWayland layer? – Kulfy Jan 21 at 7:34
  • @Kulfy Likely, yes. The quoted Fedora documentation mentions that. Nautilus may be an XWayland application, Gnome Terminal should be an XWayland application as well since it works in X11, unless there exists two versions of it. As for believing whether it's a valid bug or not, I would leave this to the upstream developers to decide. At the very least clarifications from the developers would be nice. Until then, we'll just have to rely on the cited articles. – Sergiy Kolodyazhnyy Jan 21 at 8:09
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This is by design of Wayland.

As you are using Wayland, this is expected that you can not use X11 tool named xkill to kill a client by its X resource (part of x11-utils package) here.

Also you can not use xdotool, xinput (that is good as you will have more secure GUI) here and others.

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