Axel is a Griefer who wears green and is first introduced wearing a Creeper mask, while Lukas is an Ocelot who starts off as a Lovable Coward but can become one of Jesse's most loyal friends if Jesse treats him well. If you know how well Creepers and Ocelots get along in Minecraft, then is it any surprise that Axel and Lukas have problems cooperating?
When Soren is telling Jesse about the Order's battle with the Ender Dragon, Ivor — who was established in Episode 1 to be a member of the Order back then — is the only one to not play a role in the battle. Why? The story was fake, and Ivor was the only one not cool with this fact. Since they had to have come up with the cover story before Ivor's departure (otherwise he wouldn't have known about it to turn it into the final puzzle), Ivor probably decided he wanted nothing to do with the lie and requested to be left out of that particular legend.
Why do the Wither Storm's Tractor Beams enrage Endermen so they attack it? They're fired from its eyes, and an Enderman's Berserk Button is being looked in the eyes!
Why do the Ocelots become far worse in Season 1 Episode 5 than they were prior? Because Lukas left (or was kicked out). Throughout Episode 1, Lukas was often the one to rein in the Ocelots' taunting of Jesse and company. Without him, the "Blaze Rods" (as they now call themselves) have no Morality Chain to keep them in check. This comes with the Fridge Horror that Aiden was always that deranged deep down, and we just never saw much of it because Lukas always stopped him from going too far.
A major theme in Season 1 is how legends and stories can become altered with time, and how the Order of the Stone deliberately altered their legend to come off as better than they were. The very first choice you make in Season 2 is whether or not to let Lukas embellish the New Order's legends in his book. If you do, you're falling into the same trap of fame over integrity as the Old Order. However, if you insist on the events being told exactly as they happened, Lukas can give a first (or at least second)-hand account of the events of the previous season, and the book (if published) will become a solid and unabridged source of the New Order's legend that will always exist ahead of any altered retellings.
Why does Season 2 include a stamina meter during combat? It's been 5-7 years since Season 1, and (as Petra points out) Jesse's become out of shape from running Beacontown.
In Episode 2 (if you go the Boomtown route), Jesse and Axel will talk about how mining through the stone bricks would take forever, while in Episode 3, they break stone blocks with ease. It seems like a plot hole or inconsistency... until you learn that Minecraft: Story Mode was based on online Minecraft servers. In some servers, there are some buildings that were not built by players, but are part of the server, and therefore cannot be broken. If the Boomtown buildings were just a part of the world, it would also make sense why they weren’t already blown up by TNT.
The YouTubers who cameo in Episode 6 fight with Golden Swords. Golden Play Button anyone?
Why exactly Hadrian and his cronies want the Redstone Heart so badly is never revealed. But if it could power something like PAMA, they could be planning to power something less well-intentioned with it (given their nature).
The implications of the Iron Breathtaker. For one, it's not clear whether it existed before Jailhouse Block or not but both of those are horrifying results. If it didn't, that likely implies it was created JUST to torture Radar which is messed up as is, but if it did, it's not out of the realm of possibility for the Warden to have used it on other people before.
Regardless, the whole thing is pretty scary to think about — especially for a MINECRAFT game. It's not a pleasant thing to witness at first sight but when you think about it (and/or pay attention to how Radar's affected by it right after) it just makes it all the more terrifying. For one, regardless of your choice to become an Assosiate or not, not long after Radar will even still be seen coughing after that.
In spite of the Admin running an underground prison where dozens, if not more, Overworld residents, were sent to over the years, most humans were still unaware of his existence. It's likely that nobody has any idea where the "guests" and "associates" went to, to them these people just disappeared without a trace one day and were never seen again...
The disc playing on Soren's radio ("Redstone Baby Doll") sounds like a wistful love song, 1930s-1940s style. Soren's Enderman song is upbeat, but also has a wistfulness to it. During the Episode 3 credits, both songs play. In Episode 3, either Ellegaard or Magnus die. Going by what Soren told Ellegaard before she died made it seem like the love song was sung by him to her, and the Enderman song is a farewell song to friends. No other names besides "Gary" and "Sally" are mentioned as the names Soren gave two Endermen, but it makes one wonder if he named four others after his Order friends.
