The ponies say at least twice that the Everfree Forest isn't natural. The first time it's said, you get a feeling that there's something truly supernatural and strange about the forest, and that seems to be implied several times throughout the series... but the second time they say it, they go into detail about why it's unnatural, namely:
Applejack: The Everfree Forest just ain't natural. The plants grow...
Fluttershy: Animals care for themselves...
Rainbow Dash: And the clouds move...
Applejack, Fluttershy, and Rainbow Dash: All on their own!
...In other words, the ponies think the Everfree Forest is "unnatural" because it's getting by WITHOUT pony assistance, in other words, NATURALLY, as far as the read world is concerned. Clearly, Amy Keating Rogers meant to put that in as a little joke, but like other little jokes put in without much thought put into them, it becomes contradictory with what comes later, and even before. In this case, if what's so spooky about the Everfree Forest is that it exists outside of what ponies expect of the world (and the monsters that live there, of course), how exactly will it grow and take over Equestria?
Though I have a feeling the Everfree Forest itself isn't really behind this, and that it's this new "foe" the synopsis mentioned that's using the forest to it's own means. I AM excited for this, but I'm curious to see how they go about it...