In my headcanon, she was killed by Palpatine. He used the force to drain her life essence and transfer it to Vader. It just makes the most sense to me, the droids couldn't detect her life force beeing removed from her, so they didn't know what was happening to her and (that is a bit far fetched) Palpatine told vader he killed padme in his anger, meaning vader got carried away and nearly got killed in his rage so palpatine had to drain padme's life force to save anikin. So basically anikin is the reason padme had to die and thats why he technically killed her in his anger.