Oh that. Yeah that is confusing.
It is confusing, but I think Episode 14 was designed to be confusing. There are bits of foreshadowing in earlier episodes. Yuria says she use to see the supernatural all the time back on Earth...ghosts are nothing strange to her. See seems drawn to the autopilot's room after that. When the ship goes to warp while she's there, the "ghost in the machine" comes out to say hello to her...and knocks the ship into a dimentional rift because the autopilot wasn't doing its job. In episode 12 Yuria has a dream about being a nurse at the Central Hospital a year ago and seeing Yuki in a coma, only to be confronted by a spirit of a beautiful woman before waking up. However at that same time, one of the navigation staff saw the same beautiful woman manifest in the autopilot's room.
The preview of Chapter 5 has Yuria with her hair down still and talking in an unusual way.