I have heard this happen to others, but have not experience it myself. I always recommend using 7zip to extract (and extract again) as I have never had an issue - that is if you are using Windows.
I assume from the attached pic, you are using ESX. ESX tends to flatten files (if that is the term) in the GUI listing. The GUI could be hiding/masking something (my ESX experience is out of date), so you may want to list the files using CLI.