On 1.05, not sure if this was there in 1.04.

I have a ton of lesser igni and aard glyphs, I have the diagrams to make regular glyphs however it says I don't have any lesser igni or aard glyphs in the crafting menu when I try to make better ones and I have like 30 of each lol.

I tried dropping them on the ground and picking them back up but they're still not recognized when I try to craft better glyphs.

While they did break a decent amount of alchemy with this latest patch your issue is an older one.

The issue you're running into is in game there seem to be two types of each lesser glyph stone, one will be recognized in the alchemy menu the other won't.

You can tell the difference a couple ways, one is that two of the same lesser stone will give different amount the second is they won't stack with each other.

Yeah, there are at least three different "lesser" glyphs/runestones of each class, for whatever reason, and only one (craftable) can be upgraded. Seems a bit like an oversight, methinks.

they have the same name... not sure why there would be "different kinds" of glyphs when they have the exact same name.

This is definitely a bug. There's no way this can be intentional.

surprised more people aren't talking about this issue, but then again I didn't really feel like glyphs did all that much anyway.

You only get the recipes to craft the ones above lesser at much higher levels as well.... almost until the main mission completed. Maybe why a lot of people haven't encountered this yet.

Stumbled across this problem too, but I've recognized something:
The glyphs you need for crafting the "normal" glyphs have the +2% intensity stat in the tooltip.
But there are also some +5% ones with the same name.
I've tried the +2% ones and they are fine for crafting, also the ones found in crates and stuff.
Hope it helps.