Here's why:
* Shaymin's base moveset: The Shaymin you receive via Mystery Gift is in its Land Forme. This form does not naturally learn Seed Flare. Seed Flare is a move only available to Shaymin-Sky Forme.
* No move tutor option: There is no way to teach Seed Flare to Shaymin-Land Forme, either through a move tutor or via breeding.
Therefore, the Mystery Gift Shaymin, being in its Land Forme, cannot learn Seed Flare.