Using s3cmd version 1.5.0-rc1.
Steps to reproduce:
What I would expect:
I should see that the remote file in that subdirectory should be removed, but nothing else.
What I get:
It ways it is deleting (or will delete if --dry-run is used) the directory containing that file, and the file itself.
Fortunately in testing it doesn't actually delete the directory. But it looks like it is doing so!
There are really no directories stored in S3 - only objects that happen to have names that include backslash characters. (it is possible to create an empty directory with some tools, but s3cmd never does).