In a small file, semantic indentation is beautiful. In a large file where you have to scroll and scroll to find out where you are, it's a pain. And perhaps importantly - can't be autoformatted. Your IDE doesn't know what indentation level you intended, and without braces/brackets to tell it, it can't detect errors.
There's parsing automagic wackiness if you're not careful (the famous example: country abbreviation NO for Norway becomes FALSE).
The nice feature of references is almost never actually used in practice. An incorrect or circular reference can look fine but badly break things.
Yaml typing is application (and version) dependent so not really useful.
There's more, but basically JSON, though simpler and uglier, prevents all of those. You can, and pretty much have to, use an alternative 'safe YAML' parser, but even that doesn't solve some of the problems.