I am unsure now. I received updates to a bunch of Mutter-related
packages along with Mutter itself either last night or the night before,
upgrading it from 6.0 to 6.2. I had tried the 'beta' packages earlier on
which did the same but did not fix the issue, so I reverted them back to
their originals. This upgrade, however, seems to have resolved the
issue. I tried to click through several applications that I can normally
reproduce the issue with immediately and the bug is refusing to show
itself. Even the bugs where a single click on empty space minimizes the
windows of certain applications and hovering over the edges refuses to
detect that I'm trying to resize them are gone. I'll report back if
clicks fall through again at any point in the future, but for now I
can't reproduce it anymore.

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https://bugs.launchpad.net/bugs/2026194

Title:
  When clicking on some maximized or tiled windows, focus on roughly the
  lower quarter falls to the window behind

Status in Mutter:
  Fix Released
Status in mutter package in Ubuntu:
  Triaged
Status in mutter source package in Noble:
  Triaged
Status in mutter source package in Oracular:
  Triaged

Bug description:
  [ Impact ]

  Clicking on some maximized or fullscreen windows may not respond and
  the clicks fall through to the window behind.

  [ Test Plan ]

  If auto login is not enabled, enable auto login and reboot. The issue
  can immediately be observed with first party apps such as the software
  settings GUI where apt sources, update settings, and GPU drivers are
  located. Have anything open behind it and then try to use it. Dragging
  the window to another location outside of the bounds of its default
  size and position makes it completely unusable because it clicks
  through to the window behind it no matter where you click. If the
  desktop is behind it, then the window will be usable but entities on
  the desktop will be clicked if they're located beneath what you
  clicked on in the window. This behavior is identical for any affected
  application.

  [ Where problems could occur ]

  The bug and the fix appears to be X11-specific, but that can affect
  Wayland sessions too via Xwayland. The risk here is in the sizing and
  interactivity of any X11 window. Mistakes in this area can result in
  other bugs similar to this one where the visual boundaries of a window
  do not match with its input boundaries.

  [ Original description ]

  Initially I thought this was an issue with IntelliJ and filed a bug there:
  
https://youtrack.jetbrains.com/issue/IDEA-323780/Maximizing-the-the-window-sometimes-causes-clicks-on-a-lower-fraction-to-pass-through-to-the-window-behind

  But when I had the same issue with GIMP, I realized it's an Ubuntu or
  GNOME issue instead. I am assuming this is a gnome-shell problem.

  Every once in a while, when I maximize or tile (Win+Right) the
  IntelliJ window, a bottom fraction of the window (somewhere around a
  quarter) becomes impossible to interact with, with the mouse. Clicking
  in that lower area will give focus to the thing behind IntelliJ, and
  if it's a window, raise it to the foreground. if I restore the window
  so that it is not maximized, the entire window is interactive with the
  mouse once again.

  This also happened with GIMP.

  The attached "Screencast" is a recording. I had to crop it to hide
  personal information. The attached screenshot shows the state of my
  screen so you have context, with a bright green color used to replace
  personal information.

  For the first 10s of the recording, I simply moused over to show how
  the cursor changes around a quarter from the bottom of the screen.

  For the next 10s, I left click, then move, then left click, then move,
  until focus changes to Sublime, the window behind IntelliJ.

  For the remainder of the video I show that right-clicking and mousing
  over works fine on the top three quarters, until I reach the bottom
  again, and then the right click is sent to Sublime.

  Ubuntu 23.04
  gnome-shell version 44.2-0ubuntu1

  ProblemType: Bug
  DistroRelease: Ubuntu 23.04
  Package: gnome-shell 44.2-0ubuntu1
  ProcVersionSignature: Ubuntu 6.2.0-24.24-generic 6.2.12
  Uname: Linux 6.2.0-24-generic x86_64
  NonfreeKernelModules: zfs zunicode zavl icp zcommon znvpair
  ApportVersion: 2.26.1-0ubuntu2
  Architecture: amd64
  CasperMD5CheckResult: pass
  CurrentDesktop: ubuntu:GNOME
  Date: Wed Jul  5 12:05:46 2023
  DisplayManager: gdm3
  InstallationDate: Installed on 2022-09-19 (289 days ago)
  InstallationMedia: Ubuntu 22.04.1 LTS "Jammy Jellyfish" - Release amd64 
(20220809.1)
  ProcEnviron:
   LANG=en_US.UTF-8
   PATH=(custom, no user)
   SHELL=/usr/bin/zsh
   TERM=screen-256color
   XDG_RUNTIME_DIR=<set>
  RelatedPackageVersions: mutter-common 44.2-0ubuntu1
  SourcePackage: gnome-shell
  UpgradeStatus: No upgrade log present (probably fresh install)

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