I have this same issue. My ftp account I use has full permissions. Tested this and proven.
I have also checked in the server and I do think I have ownership of the files but cannot work out if it is a system permission with apache or my ftp server. (I dont use hosting, I have it on a linux server, no cpanel. just ssh!)
It doesn't affect me much as I can access the files directly but it would b e nice to have it working perfect.
I usually get the error when I try to load "new" plugins, do updates on plugins or core updates. (or plugin deletions)
Anything that uses the ftp panel within the admin section.