Understandable, since you are viewing the film from a 2012 mentality that is generally informed about the nuances of Japanese culture.
The documentary definitely poisons the well by the disclaimer at the beginning:
"Yes, there are Japanese in our country, but they're the good ones who work hard and believe in freedom like us. Now let us show you the horrifying lives of the Japs over in the Japan - our enemies".
The WWII American public didn't have the access to explanations of Japanese cultural iconography like we do - so the nonsensical battering of images that they see, of dragon worship, high tempo marching, and rice milling, can only be seen as demonic and freakish, and therefore a threat.
I mean, dayum, that production value. I felt like I was watching The Ring.