I used to have this problem too. It took me a loooong time to figure out that my Achilles and calves were way to tight. So when my muscles swelled during exercise, they cut off my circulation.
I'm having a very hard time with week three as well. My lungs give out. What should I be doing on the off days to keep up my endurance?. Every time I attempt W3D1 it feels like I've never done it before.