I have tested this on a fresh install of Joomla! 2.5.28 using the Joomla! Update Component and following the steps on https://docs.joomla.org/Joomla_2.5_to_3.x_Step_by_Step_Migration.
I was able to reproduce the issue after upgrading to 3.4.1 - saving global configuration worked but the error showed in the "Developer Tools" in Firefox (see screenshot).
Investigating it further I came across a report on the forums (http://forum.joomla.org/viewtopic.php?f=706&t=808842) where people seem to be seeing the same issue with other components and also in front-end.
The comments on forum post hint on it being somehow related to caching and I noticed that clearing joomla cache did not solve the issue. Only when I cleared the browser cache the error message went away, not showing again while testing. I cannot assure it will not come back at some point.
Not being a JS and mootools expert myself, I'll leave it to more experienced testers to try to find the source of the issue.

I just reproduced the issue as well - although the fix is fairly easy. You just have to clear your browser's cache. In this particular case (Global Configuration not saving) the browser uses the old, cached version of /media/system/js/validate.js. Once you reload the page & clear the cache (usually CTRL+F5 in Windows browsers) everything works fine. Perhaps the docs should point this out?

Moving to Information Required until we have a respond by @HornFl4kes or @maskitto on the point by @OctavianC

Closing as requested that for the update @HornFl4kes

Why don't we add a get parameter (with the joomla version) when we include the js file to be sure not to use the cached version ?

If it's a good fix, I can do so.
What do you think about this guys ?

There are already a couple of ways in the core API to append a version to a media file, let's not add another. Especially one that uses the application version.

Oh ok. I was not aware of this sorry.
But do we agree users shouldn't have to clean their cache when a website is migrated ?