Certain videos have a domain-level whitelist or blacklist applied to them. This is done at the discretion of the content owner.
If there is a whitelist or a blacklist, and the domain of the embedding site can’t be determined (perhaps because of there not being a real referring domain in the case of your native application), then the default behavior is to block playback.
This blog post has a bit more detail as well: http://youtube-eng.blogspot.co.uk/2011/12/understanding-playback-restrictions_28.html