If this happens you can't activate the plugin/theme because the content of the ZIP file that contains the plugin/theme is broken. There are some plugins/themes around that have some extra directories in their ZIP files, e.g.:
I don't really want to support this stuff since this would lead to some extra guess-work.
I recommend this: if you encounter a "broken" plugin/theme just contact the author and politely ask him whether he might fix this. The standard layout of a ZIP file should be "[plugin/theme-name]/[files...]".




