Everything in S3 is an object. To you, it may be files and folders. But to S3, they're just objects.
Objects that end with the delimiter (/ in most cases) are usually perceived as a folder, but it's not always the case. It depends on the application. Again, in your case, you're interpretting it as a folder. S3 is not. It's just another object.
In your case above, the object users/<user-id>/contacts/<contact-id>/ exists in S3 as a distinct object, but the object users/<user-id>/ does not. That's the difference in your responses. Why they're like that, we cannot tell you, but someone made the object in one case, and didn't in the other. You don't see it in the AWS Management Console because the console is interpreting it as a folder and hiding it from you.
Since S3 just sees these things as objects, it won't "exclude" certain things for you. It's up to the client to deal with the objects as they should be dealt with.
Your Solution
Since you're the one that doesn't want the folder objects, you can exclude it yourself by checking the last character for a /. If it is, then ignore the object from the response.