Why couldn't the Ministry of Environment track down Yomi's cell phone to try and find her?
Perhaps she turned it off, she only used it a few times.
What confuses me about the whole series is...For those like myself who read the manga first, and then watched the anime. There is nothing conclusive about Yomi being beaten by Kagura, we know she comes back a few years later. Also, the fact that Mitogawa says: "Maybe the Sesshouseki gave her the choice of being killed" seems like the studio trying a bit too hard, I mean the considering that Yomi comes back sort of subverts the whole thing. — Andaria
What confused me was that when Yomi broke out of the hospital she was naked, but later she has her cell-phone, I didn't see her take it out of the hospital, and believe me, I would have have noticed, so when did she get it back?
We never saw her actually leave the hospital, so it's possible that she took it with her when she went to see her uncle, put it down before she went to threaten him, and then picked it back up and carried it with her after she found her old clothes.
Yomi wants to protect Kagura, but she's attempting to kill Kagura after her Start of Darkness.
Might be excused by the Sesshouseki being explicitly stated to warp the emotions of those who use its power in the most negative way possible. Yomi felt betrayed by Kagura the last time she saw her in the hospital, so the stone probably used those feelings to get Yomi to fight her. And each time she confronts one of her former comrades, she mentions how they did her wrong while she was in the hospital. There are times when Yomi breaks free and realizes what she's doing, and its only when her wish is in accordance to what the stone is willing to grant (i.e. death) that she's able to be killed by Kagura.
Yomi being brought back in the manga a second time for the third arc as a hero and a Yuri option to Kagura, after the rest of the manga focused on the Kensuke/Kagura match up because Kensuke was the main character... well till Yomi came back, seemed like a side character after that. Also all the hate Kensuke got from the anime fans that read the manga and saw him as trying to "steal" Kagura from Yomi for himself...
The fact that the solution to every problem that arises in the manga/anime is killing Yomi.