Sorry about the confusion. We'll be adding more explanatory in the next version.
The reason you have a mixed of max-level and need to level super plants is because of the data migration. If you have obtained the super plant in the last version, this super plant will reach max level after you upgrade to the new version. To level up super plants you need to keep collecting pieces, and it will level up automatically. Super plant will give you more energy/amethyst/ruby when you level up them. You can check the 'book' section to find out its current value.