I’m sorry to hear you’re having issues extracting your zip package.
Generally unpacking zip files on Ubuntu is fine. I just tried a package with folders to confirm it works.
How did you create the zip file? Was it created on Windows or Linux?
Could you possibly attach a sample zip file that replicates the problem, and also a full task log of the deployment please?
This happens if you use the .net framework (System.IO.Compression.FileSystem) to create the zip file (at least in Octopus v3.3.4, unsure if it’s been fixed in newer releases).