The rim on my Scott CR1 cut the rubber on the stem right where it is at the radius of the tube. I used a Qtip and checked the hole and lots of cotton came off. I only had a triangle deburring tool and not a Swieval head tool at the time, so I decided to slip a 90 durometer Oring on the valve stem before slipping the valve into the hole on the rim. It lasted until I fixed the Burr after 1k miles.

I think part of my cut were also from me pulling the valve on my tire pump every time I yank it off the presta. Instead of a straight tug, I yanked it sideways and that gets the cuts at the hole of the rim.