If you are doing what you are suggesting then you this is not a NetApp issue, but one to do with how you are using the shares, if you create two shares for example
Basically the share is only providing an access point into a directory and its subdirectories, if you create multiple shares that show the same subdirectories, then any change will be reflected in all shares. Shares are not a logical separation for file access all they are is an access point to your data directories, so for example
On a windows server you have Drive D, this drive has the following layout
D:\
D:\A
D:\B
D:\C\sub
If you then create a share that is the root of D, so share 1, when you connect to share 1 you see the following
D:\
D:\A
D:\B
D:\C\sub
If you then create a share of d:\C then when you enter that share you see the contents of directory C including its subdirectory sub.
So if you change a file in the subdirectory sub, it will be reflected in both share 1 and share 2 as in the end the file you are changing is in d:\c\sub this can then be accessed by two different shares and the changes are reflected in both.
Sorry if that seems like I’m over simplifying and you know that already, as I may of missed the point of your question.
Hope that helps.
Paul.