"The reviews of this shoe are amazing but it scares me that you say they rise high, do they rub your ankle bone at all? (Bony protrusion at bast of ankle)"

There is zero rubbing. The collar seems to be slightly higher than what I am used to, but the only time you notice it is putting on the shoe not when you are wearing it. I think the purpose from a design aspect is for a better fit. The upper material is nice mesh. You should not get any hotspots from the upper.