I have now also filed a bug report on this upstream:
https://bugzilla.gnome.org/show_bug.cgi?id=762193

** Bug watch added: GNOME Bug Tracker #762193
   https://bugzilla.gnome.org/show_bug.cgi?id=762193

** Description changed:

- I am running Ubuntu Gnome 15.04, with Gnome Shell, and I recently
- upgraded from Gnome 3.14 to Gnome 3.16, and have noticed a few issues,
- one of which I am reporting in this report. The thing that I have
- noticed is that suddenly for seemingly no reason, if I try to drag, or
- click on a window, or interact with it at all, nothing happens... And as
- I am running Docky this means that I can't even changed to a new window,
- or open a new program, instead I have to go to the Activities Overview
- which seems to still be functioning during this outage of the other
- programs. This normally only lasts for a minute or two, but is still
- very annoying. So I am reporting it as a bug.
+ I first noticed this issue when I was running Ubuntu GNOME 15.04 with
+ GNOME 3.16, but even now that I have upgraded to Ubuntu GNOME 15.10 with
+ GNOME 3.18 I still experience the issue (though I have not yet
+ experienced this on Ubuntu GNOME 16.04 with GNOME 3.19 - but that may be
+ due to the fact that this issue only comes up every so often (a few
+ times a week at the moment) and I haven't used it that much). The issue
+ being that for some reason suddenly for seemingly no reason unless I
+ interact with the top bar in terms of clicking on an option on it (e.g.:
+ the calender or Activities Overview buttons), I am unable to click on
+ any application, or even drag some files on the desktop, though if I go
+ to the bottom of my screen Docky does should which is on autohide so it
+ does allow some interaction, though interestingly not all as buttons
+ don't change colour that normally would when I go over them when my
+ machine is doing this funny thing.
  
- INFORMATION UPDATE:
- 
- I am now running Ubuntu GNOME 15.10 with GNOME 3.18 and still experience
- the issue, though less often than I did with the previous version of
- GNOME and Ubuntu.
+ Some have even said though that they have to completely restart gnome-
+ shell to temporarily get rid of the problem. I also experienced the
+ problem a lot on 3.16, but in 3.18, it is periodic in the week that I
+ experience it and it is several times, but not as much, and not as
+ blocking.

** Changed in: gnome-shell (Ubuntu)
       Status: New => Confirmed

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https://bugs.launchpad.net/bugs/1482397

Title:
  Applications suddenly don't allow any interaction with them

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