No idea why, but every single recipe in order to mutate a plant in JEI comes up with a pumpkin seed and a wheat seed. If this is a problem on JEI's end, then please tell me and I'll forget about it...since my modpack needs an earlier version of forge, if JEI is the issue, I'll just have to live with it :)

No issue here. It's just simply that all the mutations are set to use pumpkin and wheat seeds for the 1.8.9 builds. As this is a minor issue for an alpha version, this issue will be closed.

Not to worry however, as this issue will most certainly not be present in later versions of AgriCraft..