Whenever I try to make one of the super crops (putting the correct ingredients into artisia seeds and right-clicking the middle with a wildwood staff) it makes the super crop but the middle immediately breaks like I right-clicked it for a normal recipe. Am I doing something wrong?

you probably have another mod that enables right-click harvest and thats causing the problem (Pam's Harvestcraft, V-tweaks, and Quark do that, there are probably others I havent seen though)

Incorrect title- real issue is user error, stemming from the right-click harvesting feature of another mod which interferes with the way Artisia crop crafting works.

I can confirm that super crops are indeed working as intended in 0.2.1: