In thinking about the Everfree situation in this story, I should clarify what the monsters are and how they function.

When Hyperion's horn was shattered and spread over the region of Everfree, it began leaking magical energy directly from the Aether into the surrounding Lifestream. But Hyperion's own consciousness was also spread in the same way since an alicorn's consciousness is always attached to their horn, even after death. Consequently, a great deal of magical energy is under malicious control in the region.

The result was the manifestation of horrible creatures which desired to do harm to ponies in various degrees of severity. Pretty much everything in Everfree hates ponies. What is significant is that there is no balanced ecosystem in Everfree. The monsters manifest directly from the magical influence and form an imbalanced predatory relationship within their domain. They need a continuous influx of this magical energy in order to maintain their existence. If Hyperion's influence fades, the monsters diminish and fade away as well. This is why they don't generally venture outside of the forest. They would cease to exist if separated from the forest for a significant length of time.

Over the course of this story, Hyperion's influence is on the rise. This creates an interesting situation because new and more dangerous monsters are spawning within the forest. We will see these come into play in the story at the end of Act Two. But they have been spawning for a few months now, causing an imbalance within the forest which ponies are only now beginning to notice.

Generally speaking, ponies leave Everfree alone. It's been a dangerous region for long enough that nopony builds a home within the forest, and few dare venture inside. Years ago, it was not as bad, especially immediately after the Elements of Harmony were returned to the Tree of Harmony. But ponies have never had issue with building homes or farming land near the borders of Everfree. It is generally understood that the monsters within stay inside the forest and only very rarely stray out to cause trouble.

With the newer and more deadly monsters spawning, they have begun hunting the existing population of monsters within the forest and taking over their territory. As a result, the older standard monsters are being driven outward from the heart of the forest. With their safe zone shrinking in size, they've begun to venture outside the forest entirely, preferring peaceful death by diminishment over violent death by predation. This is why we see manticores, cockatrices, vampire fruit bats, and timberwolves well outside the borders of Everfree.

As Precipice opens up, our heroes find a pack of timberwolves a kilometer or so away from the Everfree treeline, invading an earth pony family's property and trying to kill them. Among these timberwolves are several larger timberwolves. These came from Everfree, and stored up the magical energy which they are manifested from prior to leaving the forest. Using this magic, they have stripped bare many of the local trees in order to breed more timberwolves, thus making a strong and numerous pack.

Overall, Everfree has permanently become much more deadly, and the less dangerous monsters are being squeezed out. Ponies surrounding the region are at the most risk, and eventually, it will become accepted that a buffer zone needs to be respected and Everfree itself should be quarantined. Those who have lived near the forest will need to retreat further away into the safe parts of Equestria.

Because this is Aether magic being channeled through a wild alicorn's horn, even the royal sisters are powerless to "cure" Everfree and make it like the rest of Equestria. It might have been possible for Luna to repeat the process and grow a new Tree of Harmony once more, but the war with the zebras got in the way of those plans, and Everfree remained permanently deadly all through the time of the Wasteland.

Little question: Will Hyperions growing strength begin to effect the Everfrees weather as well? Since its been portrayed as a pretty wild place already.

5524442 Well this might complicate things for everyone...

5524568
Care to elaborate?

5524588 I meant in an in-universe way. With the war against the Zebras approaching, I have this bad feeling that their hooves are going to be tied up dealing with that and the Everfree situation.

5524590
Ahh. Well, it's not really anything to do with the zebras. Nyx has a primary and a secondary mission, as chapter eleven pointed out. And as I mentioned above, they won't be dealing with Everfree directly until the end of act two, so not for quite some time yet. All the stuff now is just foreshadowing. Establishing the plot thread as a significant issue. I'm not sure how much to progress the problem over the course of act two. Mostly I think it'll be handled off camera by having a quarantine zone set up.