I have 14 lesser glyphs of igni and 10 axii in my inventory, however at the crafting menu it shows 0 of the required 3. I've reloaded, restarted, and even tried dropping them and picking them back up but it never registers that I have any to upgrade.

I have encountered glyphs which stack in different piles, even though they are the exact same name (e.g. igni) and same stats (e.g. 2% burning). I am guessing this glitch is related to your problem. It looks like there are two strands of glyphs in some cases, and only one is flagged for crafting.

Check it again. One of those stacks will be 2%, the other 5%. This must be some kind of bug though. Its annoying since they are named the same, "lesser" but differ in stats.

Yeh, it's a very annoying thing since it's not relevant for mutagens.. as long as they are the same colour, they can be combined.. but with glyphs, they need to be exactly the same in everywhere way.

Yea it's a design error, they didn't allow the crafting recipe to accept any other type of lesser glyph besides the one you can craft. (You can buy it off vendors too)

A lot of the glyphs you find as loot though, if not all of them, won't be able to be used in a greater glyph crafting recipe. No idea why they made multiple kinds of each lesser glyph/runestone, if they just stuck to 1 type of lesser this wouldn't be a problem.

Nope. I have stacks of 2% and 2%.