Minecraft Ender IO destroying magical crops

So, I saw some youtubers using a Ender IO farming station to automate Magical Crops. So, I thought,”hey, I’ll try and use that to get my resources more efficiently. So I grinded, exhausted most if my resources, and got my farming station, as soon as I gave it what it needed, instead of it harvesting the crops like it would’ve if I’d used my fist, it harvested the essence and the crop was gone. I was lucky enough to have some back-up seeds so I wasn’t entirely ruined, but I want to know how to fix this so I can get back on my feet, and move on.