I have the same or very similar problem on Ubuntu 16.10.

It happens usually after certain programs are run (like notepadqq,
sometimes open office or image viewer and most usually Netbeans, with
Netbeans on it's nearly certain it will happen on my laptop after some
time running, especially when there are more programs). It usually
blocks Chrome from navigating tabs, sometimes other windows from clicks
or resizing. If not with Netbeans then usually when doing something
processor and ram intensive in background (but not as much intensive to
be low on memory, like having 16 GB RAM and using 6 GB and 100% of 2
processors).

Strangefully usually closing Netbeans help for me - but not always.
Sometimes it's ok after closing but problem is back in few minutes after
closing.

It looks like it might be related to some resource in the system but I
can't guess which one.

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You received this bug notification because you are a member of Desktop
Packages, which is subscribed to gnome-shell in Ubuntu.
https://bugs.launchpad.net/bugs/1181666

Title:
  gnome-shell randomly blocks mouse clicks from working in app windows

Status in GNOME Shell:
  Confirmed
Status in Ubuntu GNOME:
  Confirmed
Status in gnome-shell package in Ubuntu:
  Confirmed

Bug description:
  Under GNOME 3, the use of the mouse-click stops occasionally, though I
  can still move the mouse around and can still click on items in the
  Activities screen and the top-bar.

  I can use alt-tab to cycle windows and can still type into already-
  active textboxes in windows, but I cannot click within the windows,
  and the mouse is not picked up at all by the windows.

  I can open the alt-f2 "run command" dialogue, but cannot type into it.

  The workaround I'm using is to open terminal (ctrl-alt-T) and run
  "gnome-shell -r", and restarting that command every time I have the
  problem again.

  Please ask if there's anything I forgot to mention.

  ADDITIONAL: The error tends to happen randomly, but it seems to happen
  upon opening a new window, changing windows, closing windows, or
  opening the activities pane (whether a change of window is thus
  instigated or not)

  ADDITIONAL 2: (sorry, it's early) The other workaround is to log out
  and to log in again, but that is also less than ideal

  ProblemType: Bug
  DistroRelease: Ubuntu 13.04
  Package: gnome-shell 3.6.3.1-0ubuntu6
  ProcVersionSignature: Ubuntu 3.8.0-22.33-generic 3.8.11
  Uname: Linux 3.8.0-22-generic x86_64
  ApportVersion: 2.9.2-0ubuntu8
  Architecture: amd64
  Date: Sun May 19 07:02:18 2013
  DisplayManager: gdm
  GsettingsChanges:
   b'org.gnome.desktop.interface' b'clock-show-date' b'true'
   b'org.gnome.desktop.interface' b'clock-show-seconds' b'true'
   b'org.gnome.desktop.interface' b'document-font-name' b"'Sans 10'"
   b'org.gnome.desktop.interface' b'font-name' b"'Cantarell 10'"
   b'org.gnome.desktop.interface' b'monospace-font-name' b"'Ubuntu Mono 12'"
  InstallationDate: Installed on 2013-05-04 (14 days ago)
  InstallationMedia: Ubuntu-GNOME 13.04 "Raring Ringtail" - Release amd64 
(20130424)
  MarkForUpload: True
  ProcEnviron:
   LANGUAGE=en_GB:en
   PATH=(custom, no user)
   XDG_RUNTIME_DIR=<set>
   LANG=en_GB.UTF-8
   SHELL=/bin/bash
  SourcePackage: gnome-shell
  UpgradeStatus: No upgrade log present (probably fresh install)

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