Even if Vincent didn't die from the environment outside Romdo, how did he survive the fall? Even if the city wasn't actually floating in the air, it was still elevated pretty high off the ground.
This is later explained as Vincent being a Proxy: as he's composed of Armita cells he's practically invulnerable to everything except UV light. Thus the fall had no effect on him at all.
What happened between episodes 4 and 5? When Vincent arrives at the commune outside Romdo, Hoodie and all the other people living there welcome him with open arms. Everyone says they're really happy to be living freely outside the city, except Quinn, who doesn't want to live like a parasite and wants to get back into the city. But in the next episode, suddenly everyone wants to go back to the dome, and they're all suspicious of Vincent. So what happened between those episodes?
It could be interpreted that the people in the Commune are just trying to make the best of their situation by constantly stating that they are free; however there are subtle indications that they all actually want to go back and aren't satisfied living in a garbage dump (such as when they initially wonder if someone will come to reclaim Pino before laughing it off).
The airship used by Riel, Pino and Vincent seems to be called the four hundred rabbits. Does this name mean anything? There was also a scene in the commune, when the boy named Timothy drew a picture of a flying rabbit carrying them all away from the dome. Does that have any meaning?
It's just the name Hoodie gave to the craft; like much of what Hoodie says it's probably just meant to glorify the craft and doesn't have any real meaning.
Are there any time skips in the series? Many of the experiences Riel, Vincent and Pino have on the airship seem to occur every few days, but it's hard to tell how they relate to the events in Romdo (for example, how long it's been from when Vincent fell out of the dome and when he returns in the finale).
In the second half of the show, Raul Creed takes over Daedalus Yumeno's research and demands that he work for him. When Daedalus snarks at him, Raul threatens him in a way that looked like he was going to rape him. Granted, Daedalus may not be an adult, but right after Raul leaves, he drops his afraid look and acts like he's the one in control. This scene was very confusing.
Towards the end of the series, Riel. Vincent and Pino discover a cave with a group of human-like creatures who couldn't survive in the outside environment, but were slowly dying from the gas inside the cave. As the trio is leaving, Riel notices that one of them may be pregnant, and sees some drawings on the wall that look like a baby in a womb. What was this episode trying to say?
Re-L can't comprehend that the creatures (who are implied to be heavily mutated humans) can reproduce naturally through sexual intercourse. As we learn in earlier episodes, all the people in Romdeau and the other human settlements are clones produced by artificial wombs, rather than through natural birth. Thus, it's hard for Re-L to get her head around the idea of a pregnancy and bearing offspring when she's been brought up in a society that produces children through artificial means. It's comparable to Brave New World and how people in that society have become unfamiliar with sexual reproduction.
What is the meaning of the names of the episodes? Examples include Tasogare, Ophelia, Shampoo Planet, and Futu-risk.
In the case of Ophelia, it was named after the supermarket the group spends most of their time in during the episode. Additionally, Re-L spends a bit of time being The Ophelia in this episode due to the episode's Proxy.