Steps to reproduce

1) Navigate to https://extranet.atlassian.com/crucible/browse/FE/trunk/test/testfiles/simple or to some directory within your repository
2) In the Tarball box, click on zip and download the zip
3) Double click on zip file and you will get the error "Cannot open file: it does not appear to be a valid archive"

If you unzip the file using 7zip and then unzip it again you will have the correct contents, so it appears that ie is zipping the file twice.