You can buy the magic upgrade, then you can purchase the whole spell for the same thing.
If you buy the stanza only, you do it from a tab called "Upgrades". You can see in the buy window that you are only getting a stanza. You can see in the "Actions" tab that you are getting some credits along with the stanza. Further, the sage tells you during mission 3 or 4 that you should tinker with the stanza system.
My 2 dappers is that Silan works excellently well, in that it weeds out people who don't pay attention.
You most certainly can buy the same spell twice!
I made a new Silan toon, leveled to 10 in magic.
Buying Heal Life 1 (stanza+range credit 2+sap credit 3) costs 23 skill points. Sap Gift and Stamina Gift cost 23 points too, but they use range credit 2; after you buy Heal Life, their cost goes down to 20. They still show that credit in their composition, but you already have it, and you are not paying for it.
Further, I buy Heal Life 2 (stanza+range credit 3+sap credit 7+time credit 2), costing 16 SP. Acid Damage 2 costs 16 SP before I buy Heal Life 2, and costs 7 skill points after that, to accurately reflect that I have acquired a number of the component credits.
You never pay for the same thing twice, although that thing might still be listed on the action and you seem to "buy" it. Again, people who don't read or pay attention, etc..