Why do you think that Metacity is the one who freezes? Have you tried
other window managers and/or sessions and this happens only with
Metacity?

The thing is that Metacity does not do anything with drag and drop so
that might be bug in nautilus and/or xserver.

Can you provide steps that I can use to reproduce problem?

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https://bugs.launchpad.net/bugs/1741902

Title:
  Drag and drop state may be freezed by rogue application

Status in metacity package in Ubuntu:
  New

Bug description:
  I had some issues with nautlilus in the past time, that of cause need
  to be resolved by the nautlilus devs, but it turns out that IO freezes
  (eg. dropped sftp connections) may freeze nautlilus while drag and
  drop operations, and hence freeze metacity in some kind, as d&d seems
  to lock some control to the participating applications.

  What I do:

  Drag a file from nautilus.

  What happens:

  Nautilus blocks for some reason, eg. dropped sftp connection. The
  mouse pointer stays in dragging state after releasing the mouse
  button. No drop action is executed. Windows can still be bought to
  front by clicking them, but never gain focus and no application
  (besides nautlilus I guess, which is stalled) receives clicks or
  keystrokes. If at some point nautilus crashes in turn, the system
  usability is fully restored. If not, a restart by hard shutdown is
  needed to regain control.

  What should happen:

  If an application fails to commence it's drag and drop interaction,
  the action should be canceled on metacity's behalf. Otherwise any
  rogue application can stop user interaction down to moving the pointer
  around, requiring hard reboot.

  Security considerations:

  Low. The freezed state seems to block screen locking, and may reveal
  an unprotected desktop if the rogue application releases control at
  some point, eg. by crashing.

  ProblemType: Bug
  DistroRelease: Ubuntu 16.04
  Package: metacity 1:3.18.7-0ubuntu0.3
  ProcVersionSignature: Ubuntu 4.4.0-105.128-generic 4.4.98
  Uname: Linux 4.4.0-105-generic x86_64
  ApportVersion: 2.20.1-0ubuntu2.15
  Architecture: amd64
  CurrentDesktop: GNOME-Flashback:Unity
  Date: Mon Jan  8 14:52:41 2018
  EcryptfsInUse: Yes
  InstallationDate: Installed on 2016-08-23 (503 days ago)
  InstallationMedia: Ubuntu 16.04.1 LTS "Xenial Xerus" - Release amd64 
(20160719)
  SourcePackage: metacity
  UpgradeStatus: No upgrade log present (probably fresh install)

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