It isn’t a bug - the initial tool was crafted using subpar materials. There’s a hidden “tax” that means you can only override SOME of those materials at any craft. After a recraft using R3 materials, you’ll notice your skill increasing as the R2 materials get overwritten.
I ran into the same problem - you can see my screenshots here as I worked it through in real time. Missing Skill Points "Recrafting" - #2 by Iskierkaa-stormrage