Adaptation Dye-Job: Many examples. Dutch has blonde hair in The Babysitter while in Halo 3: ODST, he had brown hair. Dr. Halsey has blonde hair in The Package and Homecoming, while in the books and Reach, she has black, graying hair. Fred-104 has brown hair instead of black, etc.
Anime Hair: Not surprising, considering this is an anime. In the commentary track of "The Babysitter" it's noted that real life Marines would pretty much all have buzz cuts and look like each other, but Anime Hair and different body types were used to visually distinguish them. They're also not the only ones to do this in-universe, since in the ODST series ODST troops can and do have long hair, such as Buck (given that Buck is Nathan Fillion AND a MalExpy, you don't tell him what to do).
Arm Cannon: The Prototype (Type I) and Pluton (Type II.)
Artistic License: The Hunters and Spartans are often shown as towering far above other characters, more so than in the original games (Hunters in The Duel are larger than Wraiths.) It's an acceptable break justified by Rule of Scary (Hunters) and Rule of Cool (Spartans.)
Justified: Players often underestimate exactly HOW tall Hunters and Spartans are. Hunters are 12 feet tall.
Also, Scarabs (which dwarf normal Hunters) can be considered humongous, slightly more mechanized Hunters, so it is possible that the Lekgolo worms are able to super-combine into a giant Hunter form; the comparatively smaller ones in-game are permanent colonies, while the giant ones were a special multi-colony coalition for the purpose of eliminating the Arbiter.
Art Shift: Since all the stories are done by different people, they all have varying styles, but two are of special note. The first being The Duel where the artwork is put through a filter to resemble a watercolor painting. The other one being The Package, which is an All-CGI Cartoon and thus most resembled the games.
BFS: Harka's sword in The Duel, unusual in a setting dominated by Laser Blades.
Big Damn Heroes: The SPARTAN squad in The Package, as well as the ONI Prowler that rescues them when they're being pursued by Seraphs.
Bittersweet Ending: The Package ( The Spartans successfully save Halsey, but at the cost of two Spartans), Babysitter (The ODST/Spartan squad succeed in taking out the Prophet but the Spartan dies saving one of the ODSTs) and Prototype (Sgt. "Ghost" sacrifices himself to save evacuees who were escaping).
Broad Strokes: The shorts take a number of liberties with previously established canon. This quickly became contested among the fans, though later sources managed to reconcile some of the discrepancies.
Colour Coded Characters: In episodes that feature multiple SPARTANS, they usually are wearing differently colored armor from each other so we can tell which one is which.
This was previously unlike the main canon, where The Fall Of Reach mentioned each SPARTAN looking identical with no visual markers, just their trackers to tell them apart. However, later media like Halo: Reach decided too it was unfair to keep the player guessing every time, so they too began featuring more customization.
Dual Wielding: During the large battle in The Duel the Arbiter's Energy Sword runs out of power, so he punches two enemy Elites and grabs both their Swords.
Dubtitle: Did they record the Japanese or the English dub first? In any case, the English release captions the English track on both audio tracks, making watching the Japanese track rather distracting due to inconsistent scripts (wildly different, in some cases), timing that's fine for English but horribly distracting to a regular viewer of subtitled Japanese, and very noticeable Lull Destruction.
Dull Surprise: Evident in a lot of the voice-acting in the English dub. Especially in Homecoming, where UNSC Marines who are supposedly surrounded, outnumbered and outgunned, strung-out and fighting for their lives, sound bored and uninterested.
Elites Are More Glamorous: While it does mostly follow characters not seen before, pretty much all the main characters are either Spartans, ODSTs, or Sangheili (who are actually referred to by humans as "Elites").
The Faceless: In keeping with the tradition of the games, we never see Master Chief's face.
Fanservice The first part of the Halo Legends short The Package ends with a back shot of three Spartans, John-117, Frederic-104 and Kelly-087 crouched and bent forward ready to sprint toward a large group of Covenant soldiers. Guess whose butt we have the best view of?
Flashback: There are a great many in Homecoming and The Duel, and a few in Prototype as well.
Foreshadowing : The "alien" ruins in the Heian planet. When you see it, you can clearly see the elements of ancient human architecture in them. It seems the producers were lazy, right? Wrong! Both Halo: Cryptum and the Halo: Evolutions short story "From the Office of Dr. William Arthur Iqbal" revealed that those ruins could be the last remnants of the prehistoric human civilization that once rivaled the Forerunners.
Guns Akimbo: Master Chief and Kelly-087 in The Package.
Also Frederic-104, for one short cut. Notable in that he's using a BFG Spartan Laser and an smg.
Gunship Rescue: The last-second arrival of the stealth carrier in The Package. Also horribly subverted in Homecoming, when the gunship gets blown up because the Marines won't listen to Daisy and leave her behind.
The Hero Dies: Is the case for no less than half of the shorts, with Fal in The Duel, Daisy-023 in Homecoming, "Ghost" in Prototype and Cal-141 in "The Babysitter" all dying shortly before each of their conclusions.
Averted when Frederic-104 remains behind to hold off seeming overwhelming numbers of covenant while armed only with two knives...And survives. This first since Fred is practically Mr. Knives in the novels. Anyone who read the books first knew what was gonna happen when Fred busted out the knives. Knife to see you, indeed.
The Red Elite in the Package...tossing MC an Energy Sword, when MC's out of bullets. Though he does beat him easily almost immediately after, and John is only spared by the Ship Master disconnecting part of the ship, then beaming him out.
Hot Scientist — Played fully straight with Dr. Catherine Halsey herself in the Halo Legends short The Package. You'd want to check her package out.
Especially amusing considering the fact that she's supposed to be 52 at the time... and how she looks in Reach. The producers have admitted that they let her design stray from canon for a little fanservice.
The Halsey in "Homecoming" is arguably more attractive then "The Package" version; apart from the Adaptation Dye-Job, it's at least justified by the fact that "Homecoming" Halsey is still in her early 30s.
Humanoid Aliens: In order of human resemblance, the Forerunners who speculate the Precursors influenced their common designs, the Brutes (who are ape-bears), the Grunts (who are little monkey-looking creatures), the Jackals (who have beak/maws for bitin'), and the Elites (who have a distinctive split jaw).
Four Words: He is an Arbiter. Suicide missions are what he's there for.
Strictly speaking, at the point in Elite history when The Duel takes place, the Arbiter was a station of respect and military authority. It wasn't until these very events that the title was twisted into a mark of shame, with a level of occupational hazard as sure as a death sentence. That said, Fal wouldn't have been made an Arbiter if he wasn't the baddest dude on the planet.
Also the reason that they made Dr. Halsey look rather youthful for her age (~52 by the events of The Package), according to the commentary.
Nigh Invulnerable: Pluton takes truly insane damage and is still alive in space at the end of the short after getting blasted through a Slipspace rupture.
Nice Job Fixing It, Villain: The Elite fleet master Luro 'Taralumee pulls Thel away on a gravity lift to retrieve him while their fleet escapes into Slipspace. Unfortunately, Thel was just about to kill John, but now's been pulled away at the last minute.
Out of Character: While Dr. Halsey has previously been depicted as a cold, stoic character who the Spartans see as a motherly figure of sorts, in The Package, she was put in a role of a typical Action Girl and was close to flirting with John (which adds an unfortunate bit of Incest Subtext due to the aforementioned motherly role). Not to mention that she looks far too young for her age compared with the Halsey seen in the novels and games.
Samus Is a Girl ( The SPARTAN in the first episode of Halo Legends is female. She never speaks except when her helmet is torn off, and as she seemed to have been mortally wounded, the trope seems played more so the bigoted squad member realizes that there are actual humans underneath the armor than any particular importance on femininity.)
Though his second-in-command isn't too happy with his commander not letting him kill John, due to him shouting "A thousand hells await you!" as he's pulled away from where he has John beaten.
What Could Have Been: "Homecoming", according to the commentary, nearly went in an even darker direction. Daisy was originally meant to be a Spartan candidate sniped in training by a Helljumper. A flash clone would be made of Daisy and be put in a forest near her old home, and her father was meant to believe he killed her.Imagine Odd One Out following THAT.
Worf Effect: Lots of Spartans die in Legends, Daisy, Cal, Solomon, Arthur, Ralph, etc, and not heroically either.