From your comment, it looks like you are using the wrong embed code, now you are inserting youtube, like
<iframe width="560" height="315" src="http://www.youtube.com/embed/Cw2RzvK13F4" frameborder="0" allowfullscreen></iframe>
As already mentioned, flash will not play on the iPhone, so it needs to use the HTML5 version, unfortunately, I donโt think that 100% of YouTube videos were converted, but most of them should work.
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