Multiple people upload the same file with the same name and the same content. The file is hashed as it comes in and only one copy is kept.
If the provided link is private, not index by megaupload or search engines, then it can be thought of a private locker with the key being the link. In this case it should not be Megaupload's job to know who is supposed to have the key and who does not and it seems reasonable that they would only remove the link complained about and not the content. Those other links after all could be for personal backup/use which is allowed.
Can anyone verify/deny that the links Megaupload provided were private?