The old movies Ninja Wars and Shogun's Ninja apparently contain much of the events their "shidoshi" incorporated into their own history.
I seem to remember that Ashida Kim had a history on his site that came from a bad Japanese ninja movie. Maybe they took it from there.
Here is the silly history.
http://ashidakim.com/history.html
Edit- ok, so the history you are talking about seems to be the following.
Saiga Magoichi was born to the family of Suzuki and was head of the Kishu Saiga Ninja Group. He was a master of Tsuda Ryu Kaijutsu, explosives and firearms methods as well as Saiga Ryu Ninjutsu. He based his headquarters on the Saiga Cape. There he recruited men from the Jizamurai (local samurai) from the vicinity of Saiga Castle. He was involved in the Battle of Naniwa Kanzakigawa Gassen in which Oda Nobunaga took part. Saiga employed the tactic of Shakino jutsu " flag discarding" to win the battle. The Saiga group left their own battle flags behind and moved into position carrying copies of the flags of their enemy. Nobunaga who saw his own flags and thought they were his allies (Hayes).
If so, then the source is indeed Hayes. I remember the story, but can't remember the book. And it is not surprising that there would be a movie made loosely based on the actual historical incident. There are a lot of movies made in Japan that use history as kind of a start point.
Is this the history you were talking about?