Comment 21 for bug 165113

pjman's explanation notwithstanding, this is a bug and a particularly annoying one at that.
Not fixing this for years reflects poorly on Ubuntu and Gnome.

Here is just one way the bug can be reproduced:
gksudo nautilus
copy a directory (owner is "someone", group is "someone") from one partition to another
the directory in the destination partition will have the owner as root and the group as root
right click the destination directory in gksudo nautilus go to Properties > Permissions
click on Apply Permissions to Enclosed Files
All the enclosed files will now have the owner and group as root

Now, right click the destination directory in gksudo nautilus and change the owner and group to "someone"
Click on Apply Permissions to Enclosed Files

*Now, the owner and group of the directory is changed to "someone".
However, the owner and group of the files in the directory remains root.*
This is the BUG.

The only way to change the owner and group of the enclosed files now, is to use sudo chown -R on the destination directory, because it can't be done in nautilus using "Apply Permissions to Enclosed Files"