"Miracle Fertilizer" targets the monster(s) Special Summoned by its effect, both when it is selected in the GY and while it is on the field. If "Miracle Fertilizer" is returned to its owner's hand, any monster(s) that was Special Summoned by its effect is no longer targeted, even if "Miracle Fertilizer" is activated again later.
If you Special Summon a monster with "Miracle Fertilizer", and later in the same turn "Miracle Fertilizer" is removed from the field, you still cannot Normal Summon or Set a monster that turn.
If you Special Summon 2 or more monsters with "Miracle Fertilizer", when any of the Special Summoned monsters is removed from the field, "Miracle Fertilizer" is destroyed.
If you activate the effect of "Miracle Fertilizer" and an effect is chained that removes the targeted Plant-Type monster from play, you can still Normal Summon or Set during that turn.