I have also filed a report on this issue upstream:
https://bugzilla.gnome.org/show_bug.cgi?id=761563

** Description changed:

  I have recently noticed that when one turns on the option in the gnome-
- tweak-tool in order to "Show location of cursor" when CTRL is pressed,
+ tweak-tool in order to "Show location of pointer" when CTRL is pressed,
  application are no longer able to capture the CTRL key. For instance VMs
  in Virtual Box no longer do anything when CTRL is pressed simply because
  they do not know it is being pressed, so I can't copy and paste stuff in
  VMs, nor cancel commands in Terminal, so it is very annoying. It also
  means that in Virtual Box if I press my right CTRL key instead of my
  left one (as they have different features where the left acts as the
  guest key, and the right one as the host key - the host key would
  normally be used to toggle Virtual Box capturing) it still does nothing,
  even though it's Virtual Box that should do something rather than the
  VM.
  
+ Turning off the option in gnome-tweak-tool resolves the problem, but I
+ would still like to be able to have it on without side-effects.
+ 
  ---
  
  OS Information:
  
-     No LSB modules are available.
-     Distributor ID:   Ubuntu
-     Description:      Ubuntu 15.10
-     Release:  15.10
-     Codename: wily
-     Flavour: GNOME
-     GNOME Version: 3.18
+     No LSB modules are available.
+     Distributor ID:   Ubuntu
+     Description:      Ubuntu 15.10
+     Release:  15.10
+     Codename: wily
+     Flavour: GNOME
+     GNOME Version: 3.18
  
  Package Information:
  
-     gnome-tweak-tool:
-       Installed: 3.18.0-1~wily1
-       Candidate: 3.18.0-1~wily1
-       Version table:
-      *** 3.18.0-1~wily1 0
-             500 http://ppa.launchpad.net/gnome3-team/gnome3-staging/ubuntu/ 
wily/main amd64 Packages
-             100 /var/lib/dpkg/status
-          3.16.2-2 0
-             500 http://archive.ubuntu.com/ubuntu/ wily/universe amd64 Packages
+     gnome-tweak-tool:
+       Installed: 3.18.0-1~wily1
+       Candidate: 3.18.0-1~wily1
+       Version table:
+      *** 3.18.0-1~wily1 0
+             500 http://ppa.launchpad.net/gnome3-team/gnome3-staging/ubuntu/ 
wily/main amd64 Packages
+             100 /var/lib/dpkg/status
+          3.16.2-2 0
+             500 http://archive.ubuntu.com/ubuntu/ wily/universe amd64 Packages

** Summary changed:

- Assigning CTRL to "Show location of cursor" means that applications cannot 
capture CTRL
+ Assigning CTRL to "Show location of pointer" means that applications cannot 
capture CTRL

** Tags added: wily

** Bug watch added: GNOME Bug Tracker #761563
   https://bugzilla.gnome.org/show_bug.cgi?id=761563

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https://bugs.launchpad.net/bugs/1541935

Title:
  Assigning CTRL to "Show location of pointer" means that applications
  cannot capture CTRL

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