Confirmed bug.
Mustafa, this is a bug. I have a file called test.txt with few words in it, owner is admin.
Admin -> Domains -> (selected my domain)
Filemanager, clicked the test.txt -> Edit -> Save
The owner changed to root.
Please investigate soon, this is a serious problem for clients.
UPDATE: 6.5.0f has the bug, if you edit and save owner changed to root. 6.5.1a, does not show 'owner' in filemanager, but I took same steps, logged in SSH, owner did not change. Appears is a 6.5.0f bug.