Same problem here (I think).

Stock Ubuntu 18.04.1 LTS
gnome-shell-extension-ubuntu-dock version 0.9.1ubuntu18.04.1

The dock has disappeared overnight (pretty sure that it's not related to
any updates, since auto-updates are off and /var/log/apt/history.log
does not show any installs/upgrades more recent than January 14.) I
still have a gray bar with the time on top and the word "Activities" in
the top left corner. It shows up if I click on "Activities" or press the
Windows key on the keyboard, then disappears again.

Options in the "Dock" tab in Ubuntu settings (Auto-hide, Position on
screen) have no effect.

Unlike the original reporter, my system was rebooted about 24 hours ago.

Reviewing the event journal, I see the following appear last evening:

Jan 28 21:21:56 aidev-System-Product-Name gnome-shell[3405]: JS WARNING: 
[/usr/share/gnome-shell/extensions/[email protected]/docking.js 1778]: 
reference to undefined property "_workspaceIsolation"
(...)
Jan 28 21:22:25 aidev-System-Product-Name gnome-shell[3405]: g_array_unref: 
assertion 'array' failed
Jan 28 21:22:25 aidev-System-Product-Name upowerd[2154]: unhandled action 
'unbind' on 
/sys/devices/pci0000:00/0000:00:14.0/usb3/3-1/3-1.3/3-1.3:1.2/0003:046D:C52B.0139/0003:046D:200A.013B
Jan 28 21:22:25 aidev-System-Product-Name upowerd[2154]: unhandled action 
'unbind' on 
/sys/devices/pci0000:00/0000:00:14.0/usb3/3-1/3-1.3/3-1.3:1.2/0003:046D:C52B.0139
Jan 28 21:22:25 aidev-System-Product-Name upowerd[2154]: unhandled action 
'unbind' on /sys/devices/pci0000:00/0000:00:14.0/usb3/3-1/3-1.3/3-1.3:1.2
Jan 28 21:22:25 aidev-System-Product-Name upowerd[2154]: unhandled action 
'unbind' on /sys/devices/pci0000:00/0000:00:14.0/usb3/3-1/3-1.3
Jan 28 21:22:29 aidev-System-Product-Name /usr/lib/gdm3/gdm-x-session[3271]: 
(--) NVIDIA(GPU-0): DFP-0: disconnected
(...)
Jan 28 21:22:29 aidev-System-Product-Name /usr/lib/gdm3/gdm-x-session[3271]: 
(--) NVIDIA(GPU-0): DFP-6: disconnected
Jan 28 21:22:29 aidev-System-Product-Name /usr/lib/gdm3/gdm-x-session[3271]: 
(--) NVIDIA(GPU-0): DFP-6: Internal TMDS
Jan 28 21:22:29 aidev-System-Product-Name /usr/lib/gdm3/gdm-x-session[3271]: 
(--) NVIDIA(GPU-0): DFP-6: 165.0 MHz maximum pixel clock
Jan 28 21:22:29 aidev-System-Product-Name /usr/lib/gdm3/gdm-x-session[3271]: 
(--) NVIDIA(GPU-0):
Jan 28 21:22:29 aidev-System-Product-Name gnome-shell[3405]: JS ERROR: 
TypeError: this._workspaceIsolation is undefined
                                                             
DockManager<._deleteDocks@/usr/share/gnome-shell/extensions/[email protected]/docking.js:1778:9
                                                             
wrapper@resource:///org/gnome/gjs/modules/_legacy.js:82:22
                                                             
DockManager<._toggle@/usr/share/gnome-shell/extensions/[email protected]/docking.js:1662:9
                                                             
wrapper@resource:///org/gnome/gjs/modules/_legacy.js:82:22

(I think the dock was still up after 21:22, but I'm not positive.)

There are lots of other recurrent Gnome-related errors in the log, which
may or may not be related. These include:

Jan 29 12:30:20 aidev-System-Product-Name gnome-shell[3405]: Object St.Icon 
(0x55980a2b1f10), has been already finalized. Impossible to set any property to 
it.
Jan 29 12:30:20 aidev-System-Product-Name org.gnome.Shell.desktop[3405]: == 
Stack trace for context 0x559809c11340 ==
Jan 29 12:30:20 aidev-System-Product-Name org.gnome.Shell.desktop[3405]: #0 
0x55980a0b7498 i   resource:///org/gnome/shell/ui/osdWindow.js:206 
(0x7f2bd42c7780 @ 231)
(...)
Jan 29 12:30:20 aidev-System-Product-Name gnome-shell[3405]: Object 
St.BoxLayout (0x55980a2b0e50), has been already finalized. Impossible to set 
any property to it.
(...)
(repeated ~20 times for different options)


Jan 29 12:31:28 aidev-System-Product-Name gnome-shell[3405]: g_array_unref: 
assertion 'array' failed

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https://bugs.launchpad.net/bugs/1795703

Title:
  Ubuntu Dock gets replaced with a standard GNOME one after a while

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