I'm making a thread for us to help each other with whatever questions we have about this show. It's because it's a bit hard to keep track of things at the comments section and to keep things more organized. 

I love this show to pieces despite it not being perfect and for sure there are some plot holes here and there, but overall I believe this show did its best to deliver with every bit of resources they have. I just love Circle so much! T_T

Anyway, here goes! I'll put in some questions and if I can answer them, I'll give the answer I could think of. This also includes questions I've seen somewhere else, and I have an immediate answer to. I would also add in some questions I have no answer to and hopefully you guys could help me out by answering them if you can... and then if you also have questions, do put them in the replies and then we'll try to give answer to them, so on and so forth~

  1. What is up with Woojin's picture from 2022 if he died on that year (or perhaps still in a coma)? It's the clone of Woojin, but without his memories. Circulate 3 is the first successful clone to work on the cube because he has Woojin's memories.
  2. What has Jungyeon been doing all these years? I'd say she went into hiding and improved her hacking skills. Her way of hacking in 2017 is totally "analog" style and now she's totally a badass at "digital" style hehe
  3. How come Joonhyuk, Minyoung, Chief Hong didn't know which twin Joonhyuk was in 2027? They actually are very aware which twin Joonhyuk is, it's just that they didn't spell it out to us, the audience. It was never said that they didn't know which twin Joonhyuk is in the first place.
  4. How did Circulate 3 wake up at that exact moment in 2037?
  5. Everything about Byul. I think this has no specific answer. It was never the main subject of the drama so I'm honestly fine that they only made a nod to whatever she is. But yeah... any speculations about Byul? 
I think I have more questions in my head... but I can't remember them at the time being lol
So I'm still confused about your first question, actually. The picture of Woojin from 2022... I was under the impression that these clones were born and then had to grow up. If that's the case, why does his clone look 21 in the picture in 2022? Wouldn't the clone only be a baby? And with this understanding, Circulate 3 should only have been about 15 in 2037... correct? I'm still pretty confused about a lot of plot points tbh! I think I need to re-watch the series now that it's all aired. 
This may be against the developments in science at the moment, but maybe the clones they have made are not originally babies? Like they are immediately at Woojin's age and probably would never age. The writers probably decided to take the creative license to go that route.
How did Circulate 3 wake up at that exact moment in 2037?

I've been wondering about something similar to this since the last episode aired. the memory cube would only work in woo jin's presence (with his memories intact, ofc), which I assume was somehow connected to the 'supercomputer,' but I never caught why or how "circulate 3" became disconnected from the computer in the first place...? when he initially woke up, it seemed like smart earth's system was still operational until his door slid open.
At first I thought it was Bluebird's virus that woke him up... but that wouldn't explain the door opening. 

So now the way I see it, there really is no explanation to him waking up, perhaps a minor plot hole... or at least he just happened to wake up at the right time. Then Bluebird's virus made the door to his room open, and that is how he got out and once he left the room, that is how he officially became disconnected from the supercomputer. 

But still I really love that scene.. LOL Just because of how smoothly Beta Project transitioned to Brave New World. It just felt so natural that when I realized where the scene is going.. my jaw literally dropped in amazement.
There are loads of spoilers in my comment...

1)  They mentioned that Woo Jin was the third clone, so I imagine it's one of the earlier clones.

4)  so it was mentioned in the conversation when they were talking about making another circulate that it would take "one year" so i'm guessing that there's some kind of accelerated growth in the cloning process.

5  I considered that the reason that he woke up has something to do with Byul being in close proximity, because if someone has both of them and the technology, then they could remake the memory erasing system that their father destroyed - like an anti-password that no one would figure out because it's built in. That was never explained but that's where my mind went.  it didn't happen when Woo Jin and Joon Hyuk were together as kids, but i reckon Byul has something to do with it.

So here's my question.

Woo Jin of the future is a clone, but he's still a HUMAN, if he's been lying in bed for years, even 6 weeks with no activity, how can he walk, all his muscles would be useless.

@hongberg I do too. every episode has a smooth transition from beta to brave new world, but you know it's transitioning. when he wakes up, it's literally a moment from 2017 that flows straight into 2037 flawlessly. I realized what was going on quickly enough, but just for a second there I didn't realize we were in the future segment! and briefly tricked myself into believing he was okay

if he's been lying in bed for years, even 6 weeks with no activity, how can he walk, all his muscles would be useless.
because science magic.

honestly, I don't know. I thought the same you, @Naksken. his bones and muscles would be in a weakened state from bearing no weight.
1. The said that when they first cloned Woo Jin he didn't have the memories of Woo Jin. So I am guessing that Ciculate 2 helped fund Human B, not knowing of their autrocities. Somehow this clone died (I'm assuming), and they used Circulate 3 to power the super computer. 
2. loolle probably perfecting her hacking skills so she can return people their memories, and gather clues as to where Woo Jin is, and probably eventually take down the government lol.
3. I'm pretty sure they knew they just didn't tell us...sorta ruins the mystery ya know? 
4. This is probably one the shows few plot holes. But since the show typically takes care to answer its questions and has smart writing, I just take it as a miracle ;) 
5. tbh i never cared about Byul's orgins. But I assume she's an alien, especially with that ending. 

@Naksken that is so true, that boy should have not been able to walk. haha, another one of the minor plot holes.

My question, how does the supercomputer work?? Were they able to expand it with Woo Jin in vicinity the whole entire time?? It only works for HIS memories, so I thought for sure they were implanting everyone's memories in his brain, and then that's how they got the footage...but he was just lying their peacefully. Like how does this thing work????
@KatySarang_TGeyes I just read your reply explaining the 2022 picture.. I know it's Woojin's clone without his memories, most likely Circulate 2, but I just didn't know the purpose of that photo. So thanks for the reminder that it's actually to get further funding for the project. 

For your question... noooo idea. XD maybe the memory chips could make use of the cube's software while the cube is powered by Woojin's presence? 

@airtwit hahaha I agree with you.. "science magic." XD 

I missed what happened to their dad and his relation with Byul, other than the memory thing. 
@FallingForever, their dad's fate was told in episode 11 (or 10?), I think, but:

their dad had no initial relation to byul, other than he took her in after they found her. she helped with making advancements in his and professor han's research after that, so I would guess it was more of an acquaintance/colleague, maybe friends, type of relationship? but professor han wanted to use the knowledge and tech given by byul for things that their dad didn't agree with/believed was unethical --- he erased byul's memory (per her request) and destroyed all the research. as a result, the officer who always had a lollipop in his mouth shot him dead.  
4- As I understood it, the virus made the supercomputer fail to maintain Kim Woo Jin in a coma. Once awake, he got out and then, no connexion anymore.
Hello, I just found your thread and I couldn't resist to share my thoughts. 

1) My biggest thought is what if Woo Jin is alive somewhere but without memories and why we must believe what Park Dong Gun said.
2) We saw and they told us that the alien cube works not only with the memories of Woo Jin but also with his psysical appearance. Plus, they couldn't create a perfect clone. So, I was wondering what if the main resource of Human b is ''the real but unconscious woo jin'' (in another facility) in order to have all of his memories, and the clones itselfs are the way to have his younger face like an ID for the cube. 
3) If my second thought is right then this could explain how circulate 3 woke up and why he has all the memories of woo jin. Also, we know that the cube has unlimited abilities and that's how the memories transfer into the clone brain.
4) What if they kill him (back in 2022) but as I said we found that the cube has lots of abilities and one of them is the ability to transfer all the excistence of a human in a virtual reality. Of cource they buried him (as they told us) but this also explain why the system work all these years and why woo jin's clone have all these memories and all these emotions. As a result, he isn't a clone but the real woo jin in a new body. (I came with this theory because I am a huge fan of ''Battlestar Galactica'' and if you know the story about ''Cylons'' you will understand my speculation).
I agree with you all. Woo Jin of 2022 was Woo Jin without memories. For me, he was the first Chairman (that explain the photo) and, if you know his research, he wanted to make people with PTSD forget their painful memories. But i guess that that Woo Jin died (murdered) soon after he discovered the true purpose of Park Dong Gun.

And for this not happen again, they opted to leave in a coma state to not disturb with the major plan. But, after the Bluebird virus, he woke up and, after he distanced hiself from the wall and the bed the supercomputer was disabled. (Park Dong Gun circumvented the room to get the cube in the other side of the wall of Woo Jin's room).

Just finished  liked it very much  but there are lots of plot hole and unanswered i totally ignored them. 

One thing  don't  understand  WHY  "Park Min Yeong" got operated in  ep12 ? plz anyone explain.