Here's an example of how far the government stretched the truth in order to get the warrant. According to Dotcom, in a previous investigation: "The FBI asked us for uploader information regarding 39 files and told us to keep their investigation confidential. We assisted and obviously didn’t touch the uploader accounts or files because of the ongoing investigation,"
The US government then used the existence of those files 2 years later as part of the evidence for the warrant to seize all of Megaupload's servers. Megaupload was never told to delete the files, and was afraid doing so would interfere with an investigation.