The B-17 guns could have all been out of ammo.
The guns on the B-17 usually had a minutes worth of ammunition:
http://www.b17.org/history/specs.asp
Imagine flying all the way to Schweinfurt and back being harrassed by fighters most of the way. There's a very good chance you are going to run out of ammo especially if you lose contact with the formation and you are on your own. The footage does show that this bomber is alone.
50 cal ammo weighs a lot so you can't take that much with you.