Last night i did two upgrades of real live websites. From 3.3.2 to 3.4.1 using the auto update.
While the update didn't show any errors and finished (and 3.4.1 was on the lower right), the result was a mess. Many files/folders didn't update.
I had to manually upload the files and overwrite.
And please do not suggest to check my permissions.
And i found it out because Osclass after the update told me to upgrade Bender (!). So i checked and found old files and folders.
upd: We are now restoring 3.3.2 fully, since something is not right and i;m afraid the DB also has some problems after updatings. Not sure but better to be safe.