Any continuity "flaws" in the show will probably be rationalized as alternate universe glitches. While closer to our universe than the "red" one (obviously coffee is readily available in this one), it's still slightly different and using a cellphone app to buy coffee is a common occurrence, but Walter isn't exactly…
That bugged me too. If the nanites were activated by motion, well, blood is in constant motion in the circulatory system. If they are triggered by some pre-determined increase in that motion (like an increase in blood pressure, heart rate) or an increase in adranaline, well, the ones standing still were still under…
I'm sure J.J. has some left over "Alcatraz Juice" lying around somewhere...