I have had this issue as well as another topic I have read here, and I was not sure if it was just something with Windows server or WordPress.
I have had this when updating two plugins and the twenty eleven theme.
This is what happened in my case, the plugins 'include' folder and the themes 'inc' were not deleted, could this be because a script in the folder was in use on the admin page?
If I am upgrading twenty eleven from admin then I am using the files in the /inc/ folder.
When the update tries to copy the flies access to the include folder is denied.
Using FileZilla the folder still exists but will not delete or rename.
The file could also be seen in the ISP control panel File Manager, and could not be accessed, renamed or deleted, although file permissions are correct.
A manual transfer of files and it looks like a file cannot be replaced and causes this problem.
I have to wait 30 minutes for error to clear and the folder to dissapear, so I am not sure if it is a WordPress or Windows server problem.