I don't think the behavior is wrong, but yeah may be slightly confusing.
You cannot have two wiki pages with exact name. That's a fundamental technical restriction.
If you were allowed to successfully upload the file (whether it's truly duplicate or not), that means we will have these two pages sitting on one title:

1. File:Logo.png - the redirect page
2. File:Logo.png - description for your new file

The error message might be slightly off the mark by assuming that if a title exists, then anyone attempting to upload to that title is uploading 'duplicate' of that file. The message key is more accurate here: file-exists-duplicate. Maybe the message should be reworded to just tell what it actually know about the situation - that's the target title exists.

I don't think this has anything to do with redirects or having the same name. It's just that the existence check includes foreign repositories such as Commons (which is reasonable, we want to warn users against locally uploading something they would already be able to use) and the wording isn't really adapted to that situation.