Refreshing doesn't always work for getting the points. I would suggest, those going for the challenge, do as much as you can before reloading, don't worry about it not counting it properly, just GO!
Fix the movement.
Fix the body part counts (I played up until the 4th city, and it didn't count ANY of my shots, except for the ones from the last game where I reloaded mid-level, for some reason THAT counted it).
1/5
Yeah, the whole Epic difficulty, Guardian-being-able-to-shrug-Seal/Stun-and-bypass-Barrier/Protect thing has gotta go. I know it's supposed to be difficult, but it's kind of ridiculous when the game isn't even keeping check of the buffs properly.