When a flower grows, you must pluck it before you can use it. To pluck the flower, left-click and drag it onto the asteroid it grew on. Then it starts floating around the asteroid.
If you only just got flowers, you will only be able to use them on defensive trees for now. Move the flower to an asteroid with a defensive tree on it. When the flower arrives, selecting the asteroid will reveal a new button in the bar at the bottom.
Click that button, and the flower will plant itself next to the defensive tree. Then a mine will start to grow. :>
