I have antimatter and over 400 Thamium9, and in the bottom right corner it's telling me to create a warp cell out of them by clicking an empty slot in my inventory. But when I do, there's no blueprint. Is this a glitch?

You have to learn the blueprint first, just like you were taught to craft the jumpdrive (If you pre-ordered you may have skipped the latter). The game led me to a outpost on a planet in the system I was on that had an alien in there that taught me how to make one.

If you are clueless and you don't have any special markers (Such as a red building icon or a green building icon), go into space and do a system scan (C by default), it should add a marker for you.

It can be anything, a radio signal, beacon or something else that will lead you to it.

Edit: I see you made another post about this. It should never be a questionmark icon, the location has to be detected by a system scan or other breadcrumb trigger.

This story mission will call your attention specifically by highlighting an outpost on a planet and tries to keep it as visible as possible.
You have to go to that specific outpost to get the warp cell blueprint, and then use E on a slot to craft it.

Sigh, yeah I'm pretty confident I'm screwed here unless they make a patch for it. Thanks anyway guys

A patch for what? There should be a marker for the blueprint when you're in space.

No marker, or blueprint. I can't even find the area I started in