Gnome shell inverted clock

This looks like a bug. If I enable seconds to be displayed with the hours and minutes using Tweak Tool, the hours and minutes are correct, but the seconds are now placed on the left (using 20:45:18 - H:M:S).

I would definitely file a bug report here: https://bugs.launchpad.net/ubuntu-gnome/+filebug

Since this is trivial to reproduce, I will triage it for you so a developer who knows a bit more about this can take a look.

There was one similar, but unrelated bug report I found upstream: Bug 743821 - change in the places of time slots on Arabic desktop.

Best guess at this point is that the time is being split by the colon, and the last piece is moved to the beginning and in your case, the minutes are moved to the beginning:

1 -> 20

2 -> 45

3 -> 18

Becomes

1 -> 18 (3)

2 -> 20 (1)

3 -> 45 (2)

And the really interesting thing is, the lock screen does not have this problem.

1. Install the package dconf-tools from the Ubuntu repositories(available on Software centre). This installs the dconf-editor which is needed for changing the configuration.
2. Open dconf editor from the Dash or dconf-editor from the shell. In the editor, navigate to com.canonical.indicator.datetime.
3. Change the time-format field to custom.
4. In the custom-time-format field, change the value to the desired format. The format can include both the date and time specifiers. This format uses the same specifiers as that of the C standard library function strftime().

eg:

%Y-%m-%d %a %H:%M

2015-04-01 Wed 23:45

Alternatively, you can try commands in terminals to so the same as follows:

gsettings set com.canonical.indicator.datetime time-format 'custom'

gsettings set com.canonical.indicator.datetime custom-time-format '%Y-%m-%d %H:%M'