The Nightmares you encounter in the town look a bit different than the Bone Fiends that pop up from the ground after leaving the town. Wraiths and zombies, respectively, but why aren't they all the same? It's possible that Ruby was either not the first victim of Sunny Town or not the last, and the wraiths could be the original cursed ponies, while the 'Zombie' types are all their subsequent victims.
Ruby's last words in the game: "See you later, friend." Not "goodbye," "see you later."
Zecora seems to know about the Nightmares, assuming that's why she told Twilight and Applebloom to get out of the forest before night fell. One can only speculate what her relation to that village is.
It would also make this the second time at this point in the series where Zecora decided that keeping to her Rhyme Scheme was more important than coming out and saying what the problem actually is, the first being Poison Joke. For example: "Careful, there are actual literal undead wandering around and they might try to kill you," is a lot more informative than what she actually says.
Some players might not have questioned the amount of trees knocked down in the beginning, as it's a typical Broken Bridge to make you go further into the forest. But considering that we see Ruby in the area almost immediately after, and she says she was "just curious" about Applebloom, it's likely she was the one who knocked down all those trees.
Upon playing the game again, it's more than a little suspicious how Roneo wanted to give a ruby to his love. The murdered pony's name was Ruby. What was just an innocent fetch quest might have actually been related to Ruby's murder. After all, Ruby tells Apple Bloom that she was really good at finding things. Maybe Ruby was the one who actually found it for him the first time around, which led her to realize what she was good at...
