Apparently if you use fire it turns red, blizzard blue, thunder yellow, and Gravity becomes purple. I haven't tested Aero, or Stop yet (just started PC version so not far enough for Aero to do damage) and it seems to be impossible to cure the flowers. I tried doing 1 of each magic to see if did anything but so far nothing. It just gets heartless to stop spawning in the room as before you get to hollow bastion powerwilds will still spawn in there (at least on PC) but after Hollow Bastion I know that room stops having enemies all together
EDIT::/ UPDATE I got further in the game on PC and Stop magic ALSO works on the plants, turning them green when they bloom. I still haven't gotten a 2nd level Aero spell so it doesn't do damage yet so not results on if that does anything. However something else I noticed, when you are later in the game there is a flower by the wall to the path to go to the tree house, but earlier in the game there isn't on there. I don't know if this is an issue with the PC port or if another flower appears later. Considering there is now 5 confirmed colors, Red, Blue, Yellow, Purple, and Green it could be you need to make a flower of each color?