So, I bought the diagrams for some glyphs and runes so I could upgrade all the lesser and regular ones I find everywhere. Unfortunately the crafting menu always show I don't have any runes (or glyphs).
Buying the ingredients for a lesser rune and crafting that creates a new stack of lesser runes, which counts in the crafting menu.

Is this a bug, or is there something I have to do to be able to craft with all runes?

I think everyone has this. Either it's a bug or a really annoying feature.

Rune crafting has been a total mess for a good while now. I've never managed to craft anything in those. Money wasted getting all those recipes until CDPR fixes it.

There are two versions of the lesser runes/glyphs, the 2% bonus ones you can craft and buy from merchants, and the 5% versions you can loot. You can craft with the 2% versions but not the 5% versions. At launch the game didn't have rune/glyph crafting, it was added in a later patch. When it was patched in, the patch didn't update the looted runes/glyphs. Hopefully it will be fixed soon.

The only time I managed it was by building them from scratch. So you build the lesser runes, then you build the regular runes, then the greater rune. It was costly but by then I had lots of cash, so it didn't matter.

Some of the glyphs that I have are 2%, but still uncraftable, so I guess the ones you can find have been nerfed.

This doesn't work for me... looted, crafted, all glyphs/runes end up in the same stack and do not count for upgrade purposes. It is super-annoying, as I have loads of these that I can't do anything with.

I have also had SOME success with this method but NOT consistently.