I’ll comment as I’m the one that designed the hardware. 
. The PWR_FLAG marker is an idiosyncrasy of Kicad, its a requirement to label any net supplying power with it to pass ERC.
I did follow the calculations and layout guidelines for the mcp16301 closely, although I will likely go through it all again. I do not have any decoupling caps on the argon side, Vusb has its own 0.1uf on the argon itself which I thought was enough. Perhaps that was a poor assumption.
I suspect it could be the saturation current rating of the inductor, I will have to go through some datasheets again when I get home tonight.
I did design the power supply with a 12v input in the calculations, and the battery is actually as high as 13.3v fully charged I think.
Yeah… I should add a diode OR to vusb.