Steps to reproduce

• Open the AJAX theme builder
• Select a theme - doesn't matter if it's Default or Bootstrap or whatever
• Click Start Theming
• Click Download
• Name the download
• Open/extract the zip

When the zip is opened with SecureZip, it reports 9 errors. When extracted with any zip utility, there are duplicate files in the zip. I think the files should be in folders within the zip. Attached is one such file. I've tried this several times with different base themes.