In "Terror Firma" the superorganism doesn't seem to ever use anything but direct attacks on Drednok. This is because his android mind is incapable of being read by whatever telepathy the organism has to understand the other victims of its illusions.
In "Kobayashi Maru," Hologram!Spock interprets Dal's lament of "If only we could get off this stupid bridge!" as an order to beam aboard the Klingon ship, where Spock becomes a Hypercompetent Sidekick in the ensuing melee, and then when Dal fails the simulation again, gives Dal some much-needed mentoring. Evidently the Kobayashi Maru simulation has been modified a bit to help develop officers who get stuck on it, rather than simply beating on them as it was originally designed to do. Starfleet clearly sees no purpose in breaking their trainees, so the simulation offers them a hand when it senses they've hit the Despair Event Horizon.
Fan nostalgia aside, why does a 24th century version of the Kobayashi Maru depict the enemies as Klingons, who are (usually) allies of the Federation in this era? This could imply a further souring of relations between the two nations (who briefly went to war with each other before the outbreak of the Dominion War), or this could be a non-standard version of the simulation, akin to a fan project. Given the possible crew choices, the entire simulation is already an Anachronism Stew anyways.
Alternatively, it's still the old version that Starfleet used for decades, simply because "if it ain't broke, don't fix it". Logistically, there's no real need to reprogram a simulation most cadets face only one time, plus the Klingons are generally the most formidable, but predictable enemies the Federation has faced (they don't have a strong tendency towards advanced prototype weapons, they have a fairly straightforward tactical plan, their ships are the ones the Federation has the most data on, etc). It may even be that the Klingons are quite keen on being the hostile ships in that simulation, because, if nothing else, it can teach Starfleet officers a bit of their way of thinking ("It is a good day to die", and their much more pragmatic view on allies)
The Klingons might even be flattered that the Federation uses them as an example of an unbeatably formidable foe to humble their young officers with.
After Dal's first run on the Kobayashi Maru training simulation, he net's an extremely low score. The reason why? Dal's first instinct was to abandon the Kobayashi crew to their doom. And since Starfleet and the Federation consider it an obligation to respond to a ship's distress call, choosing to outright ignore a call for help is not an option. Which also explains why the holo-crew almost instantly start to turn against Dal when he proposes the idea.
Why are there so many Alpha Quadrant species even though it set in the Delta Quadrant? It is because the one who brought Voyager there (AKA The Caretaker) was at it for a long time before his death and unlike Voyager, most of them are probably still stuck there.
The "Star Trek Logs" Instagram page reveals in a log from Admiral Janeway mentions an illicit transwarp network and a power vacuum from her taking down the Borg Collective. Presumably folks have been using the Borg's old Transwarp technology to travel across the galaxy. Similar transwarp conduits have also been seen in use in Star Trek: Picard a decade or so later.
How does Gwyn manage to speak Dal's language in spite of having no information about his species? Because Dal's first language is actually Ferengi.
In "Starstruck", Dal assumes Holo-Janeway is lying about the Federation and that they're just self-serving powermongers like the Diviner, so he heads towards a red spot instead. This makes him look Too Dumb to Live, since he's been living in a dangerous Asteroid Mining slave camp for long enough to know red usually means "danger"... but he's also fully aware of just how dangerous the Diviner considers hope. Since he assumes the Federation has similar views, he probably figures the red spot might indicate things a despote would consider dangerous, like freedom or hope.
Gwyn sees a reflection of Zero, a Medusan, in Dal's Comm Badge. That it was only a reflection spares her permanent, lasting harm. Much like how Perseus was able to fight Medusa using his shield as a mirror.
The reason why only Admiral Janeway is the only Voyager crewmember seen attending the christening of the Protostar and congratulating Chakotay? It's likely everyone else was busy working due to their own promotions.
"All The World's a Stage" has a lot of fun showing outsiders trying to interpret what they know of Starfleet through their limited perspective and many years of oral tradition. Once the Protostar crew find the shuttle Galileo and the recording of Ensign Garrovick, we realize that this was a Lower Decks plot from the perspective of the planet of the week. The doomed Redshirt was all but forgotten and his fate unknown to the Federation, but he is venerated as a hero in the small corner of the galaxy where he did his best to help.
The two-part season ender provides another reason why Starfleet abandons the Romulan Relocation: a whole bunch of their ships get their butts kicked (some outright destroyed) by the Living Construct. This, plus the Synth Rebellion, constitutes a serious one-two punch for The Federation when they're still picking up the pieces from the Dominion War. And amongst those ships, it may include their flagship, the Enterprise-E and even Sisko's prized warship, the Defiant herself. If the ships who saved Starfleet countless times fell because of it, Starfleet would not want to take the chance of that happening again. They did send the original Enterprise packing during the Klingon War back during the 2250s so she would keep the flag flying if they did fall, and with the F coming soon, they would no doubt make sure she's not capable of being hacked in a manner like that.
As the Construct appears to be artificial intelligence, not to mention the Drednoks, the whole Order mess may have also contributed to the Ban on A.I.. It may also be why holograms don't seem to be included, as the only AI being the kids had a positive experience with was Holo-Janeway.
The main theme is orchestral - as usual for the franchise - and keeps building to a big, dramatic climax that never actually comes. In fact, it goes downtempo. Perfect for a show about kids exploring their unrealized potential.
"A Moral Star, Part 2" ends with the USS Protostar setting a course for the Federation, the USS Dauntless picking up the signature of the Protostar, and Admiral Janeway ordering a rendezvous course. She has no way of knowing about the malware program that the Diviner installed on the Protostar or the havoc that it's designed to wreak. Dal and his crew don't know about it either; only Gwyn found out, and her memory of being told about it was wiped. When the two ships finally meet...
Also in the finale, Adm. Janeway mentions that she is going out to find Capt. Chakotay, who was flying the Protostar. We've seen that the ship was invaded by Drednok during its time away, so this would mean Chakotay was either captured or killed during the takeover.
The crew and the liberated miners fly away, leaving the Diviner apparently alone to babble in Medusa-induced madness for the rest of his days... which, if he's truly alone, won't be that long. Depending on what his physical needs are (hunger? thirst? suit fluid replenishment?) the Diviner would likely die in a matter of days without any assistance. It's not that he's done anything to warrant better treatment, but it is a pretty dark fate that the heroes of this children's show have left him to.
Mitigated by the fact that Admiral Janeway found him in stasis. Between overall Federation altruism and the fact that she has no idea who he is or what he has planned, she's certain to revive him (or at least try).
She does indeed revive him, but he has lost his memory, at least until it is restored by The Vindicator, who has secretly infiltrated Janeway's crew disguised as a Trill officer.
Of the hundred Vau N'Akat that entered the anomaly, only two (The Diviner and The Vindicator) are known to have survived, but it's possible that more could've ended up at literally any point in time and either failed or abandoned their missions in the past or are lying in wait in the far future. Even if the Diviner and Vindicator are stopped, there's no telling just how many more are still out there hell-bent on destroying the Federation, and they could appear at any moment.
Janeway tells the Protostar crew that Dal will likely never be able to join Starfleet due to being an augment. Remember that this takes place not long before the synth attack on Marsand it was mentioned in Star Trek: Picard that Seven of Nine was refused into Starfleet for being an ex-Borg despite Janeway's insistence. Given the dark era that they're about to enter where neither Janeway or Picard have much influence (which canonically lasts fourteen years), things really don't look good for Dal. (Fortunately, Janeway has just enough pull to make Dal and the other prodigies*save for Gwyn, who goes to Solum to unite her people and prepare them for First Contact Warrant Officers under her command.)
There's a good chance that amongst the wreckage of the ships the Living Construct destroyed, it may include the Enterprise-E and the Defiant. We know the big name TNG veterans survived since they're due to appear in Picard Season 3, but if their baby was destroyed again, it leaves a lot of bad implications for the now pacifistic Worf and why he may have decided to give up his warrior ways. Beverly might have taken that whole experience poorly and decided to leave Starfleet for good because she witnessed her own people turning on each other (albeit not by choice) and taking innocent lives, motivating her to help out beyond the stars. Picard, Riker, Troi, and Geordi (the latter per supplemental material) had already left, and Data's subconscious was lightyears away on Coppelius, but imagine their shock if they learned that the ship had been lost and their friends had nearly been killed. And if the Defiant went, what fates awaited the Deep Space Nine crew that went onboard to help their friends? What if Kira decided to command that mission and the Defiant did indeed go down?
Fortunately, Picard season 3 reveals that the Defiant survived and is currently preserved in the Fleet Museum. And supplementary tie-in information also mentions that whatever caused the Enterprise-E to go out of service was years later than the 2383 time-frame of Prodigy's first season, meaning that she survived the battle against the Living Construct as well.
in a log from Admiral Janeway mentions an illicit transwarp network and a power vacuum from her taking down the Borg Collective. Presumably folks have been using the Borg's old Transwarp technology to travel across the galaxy. Similar transwarp conduits have also been seen in use in Star Trek: Picard a decade or so later.