I hope you can amend this without going to the entire sequence again.
What you did was obviously scanning with your composition scanner, that way you found a new Guardian Site (Codex!) and hence the Codex discovery.
What you should do is scan the glowing orb that comes out with your
data scanner!
It works like this: First you jettison a Guardian Relic (this is no material it is cargo but you SRV can hold 2 units of cargo). Just drive on the X and jettison the Relic. Now watch the orb coming out, this takes around 30 seconds or so. Go to your
turret otherwise you cannot scan. From your turret use the data scanner. You should also see 'PUBLIC data point' in your UI. This brings you to Module Blueprint. Be careful to wait until the orb is completely out and is target-able or would not receive data.
Look at this video, here you can see how to scan the Orb.