I can repro this...also happens with any of the pulldown menus.

Reveman, any thoughts on this or should I have TimZ look into this from the Chrome end of things?

Tim Zheng will investigate.

exo::ShellSurfaces that have a parent window should never show up in the shelf. This will be tooltips, menus and other kinds of transient windows.

Basically, any window that has a transient parent should be ignored by the shelf. wm::GetTransientParent can be used to check for this.

These tooltips and menus somehow don't have transient parent from my tests. These aura Windows don't have transient manager on them.

We set transient parent here:

https://cs.chromium.org/chromium/src/components/exo/shell_surface_base.cc?l=1598

It will be set on the native window for the widget.

The following revision refers to this bug:
  https://chromium.googlesource.com/chromium/src.git/+/b00685e3086d848573b29034450a44e612eafb8f

commit b00685e3086d848573b29034450a44e612eafb8f
Author: Tim Zheng <timzheng@google.com>
Date: Fri May 04 19:33:20 2018

Filter out tooltips and menus from shelf items.

BUG= chromium:839149 
TEST=Verified manually on an eve device.

Change-Id: If25b73896c7049f20c565621c9c50aad39709acc
Reviewed-on: https://chromium-review.googlesource.com/1043357
Commit-Queue: Tim Zheng <timzheng@chromium.org>
Reviewed-by: Michael Wasserman <msw@chromium.org>
Cr-Commit-Position: refs/heads/master@{#556149}
[modify] https://crrev.com/b00685e3086d848573b29034450a44e612eafb8f/chrome/browser/ui/ash/launcher/crostini_app_window_shelf_controller.cc

 Issue 840225  has been merged into this issue.

Re-opening because of a related issue that several people have noticed. Switching windows while a menu is open doesn't close the window, and it stays on top of other windows. Tim, could you take a look? Thanks!

Menus not being dismissed is  issue 788782  and not really related to this issue. Fixing that for wayland apps is not too difficult. For x11 apps is harder.

Ahh, I hadn't seen that issue (and failed to actually re-open this anyway), thanks for the link!