This post describes a by-design behavior. The following site gives you deeper information regarding this behavior: http://blog.krichie.com/2007/04/05/beware-of-cascading-deletes-in-wssmoss/
This behavior appears when permission inheritance of site in the hierarchy of a site collection has been changed. People suddenly are able to access private documents of other people.
When the inheritance permission, on a site, is set the its original value, the permissions on all children (and grand children, grand grand children, and so on) are set to the original value, i.e. “Use same permissions as parent site”.
/SubsiteA/Shared Documents/FolderA /SubsiteA/Shared Documents/FolderA/DocumentA /SubsiteA/SubsiteA1/Shared Documents/FolderA1 /SubsiteA/SubsiteA1/Shared Documents/FolderA1/DocumentA1
The only way, out of the box, to get them back is a database restore.
You can find tools on the Internet to restore/import permissions from a database restored in parallel.
For example, a search on Bing with the following keywords will give you interesting results (security permission sharepoint clone).
By Yamine Taïeb - SharePoint escalation engineer