Story of the Blanks/WMG
Story of the Blanks takes place in the same universe as Super Filly Adventure.
The Bloody Hooves in the "Blank Flank" ending in Super Filly Adventure look similar to Sunny Town's Nightmares. In both games, these creatures live in the Everfree Forest. They could be related groups, or even one and the same. Perhaps the "Blank Flank" ending of Super Filly Adventure is actually what happened after Story of the Blanks?
Sunny Town was hit by a widespread case of Cutie Pox.
This would easily explain the villagers' horrific reaction to Ruby getting her cutie mark: to them, it was a symptom of a disease that had caused all sorts of trouble in the village before. As such, they killed her to prevent that plague from spreading through the village again. Nice job breaking it, ponies.
- My belief is that the town was founded by Cutie Pox survivors (possibly young children who got the protection of a third party), and the truth of the matter became distorted through generations of retellings combined with the first hand accounts being done by panicked young children.
As a ghost, Ruby is somehow "Stuck" and can't properly learn from her actions
Ruby honestly didn't seem to expect the Nightmares to turn on Apple Bloom -- she talks about how she's sorry for getting Apple Bloom into this in a way that suggests this was nowhere near her plan -- but the Nightmares outnumbering the townsfolk and Mitta talking about how it's been happening again and again seem to imply this has happened before. One possible explanation is that Ruby has doene this before, but something about her ghostly state keeps her from learning from it -- she can't fully grasp that her trying to make friends leads to said friend's horrible deaths and undeaths.
This is the first time Ruby has actually lured someone to the town
As another possible explanation for the above issue, it's possible that Ruby hasn't actually lured anyone to the town before -- previous victims stumbled upon it on their own and attracted the attention of the Nightmares. As for why she'd lure someone this time...
The previous victims had their Cutie Marks
This can work as either a corollary to the above, or as a stand-alone WMG. The previous victims who end up as the Bone Fiends had their cutie marks, and were thus likely immediately set upon by the Nightmares. Either Ruby hoped things would turn out differently if she brought a blank in, or seeing a blank piqued her interest and she decided to lure her to the village, hoping that someone without a cutie mark would be safe unlike those who previously stumbled upon the village.
This actually is the first time this has happened
Mitta's complaint about this happening is simply about their being forced to relive the day of the party and Ruby's murder over and over again. The Bone Fiends are presumably victims predating Ruby and whatever curse her murder called down, or perhaps ponies who fell victim to other dangers in the forest -- there's nothing that says the Nightmares can only raise ponies they kill.
Featherweight will go to Sunny Town.
The Canterlot Royal Guard has blocked off all access, except for air. His wings are too weak, so he hires a flying machine pilot. The pilot leaves, and Featherweight has three days to get the scoop of a lifetime. He's covered food fights, y'know?