Split this to its own topic, since it didn't have much to do with Madoka, Misaki and Ruka's Getsuyuu Syndrome.
Did You Haibara's ghost really killed him with a knife? How can that happen?
No, the real You Haibara stabbed him back in 1972, and both of them died in the fall from the roof. Now they're both ghosts repeating their last actions.
Sakuya was comatose according to the game, but if she was comatose, why was she roaming the island?
She was in a coma after the Kiraigou/Ceremony of Passage, between 1970 and 1972, but she woke up on the Day Without Suffering. You actually see her waking up in one of the cutscenes; I'll try and dig up a link to a video of it on YouTube.
ETA: Here we go.
What happened to Madoka? She falls down in fear as two ghosts come near, and then become a ghost. But does it mean that she died? How? Not all ghosts are of dead people, there are ghosts of alive people in the game.
Unclear. I personally think she died then and there, but some people think she somehow survived that and kept wandering around for a while, then died later offscreen.
There aren't really any ghosts of living people. The closest things are the visions the girls see of their childhood selves running around, but that's partly explained by the fact that the Camera Obscura in this game is meant to reveal the past, and partly by the idea that their souls might have been split when the Ceremony of Passage failed and they all lost their memories, similar to what happened to Yae in FF2. All the other ones you see - You, Choushiro, Sayaka, etc - are actually dead.
Misaki falls down in the Moon Reflection Cave and the door closes. What happened right after that?
Presumably she was spirited away, since she's gone when Ruka gets there soon after, but since she's shown waking up and escaping in the Hard Mode ending, she didn't die immediately.
Madoka's surname is Tsukimori. Was Madoka also a Tsukimori clan member?
Also unclear. I personally think not, based on a couple of things:
- her surname is written 月森, whereas the Tsukimori shrine maidens wrote it 月守
- the name doesn't necessarily imply affiliation with the Tsukimori shrine maidens, since Sayaka and Ruka have the surname Minazuki and that's not said to be unusual
But the game never said, and when someone asked Shibata about it on Twitter he didn't give a definite answer. So you can make your own mind up about that.