In Fall of Reach, the Pillar of Autumn is in orbit by August 30th. However, in Halo: Reach, the Autumn is in drydock.
This one is not likely to be an error. Personally, I'd write this one out as a retcon, but some members of Halopedia has found a way to make both events possible by saying that the Autumn was grounded only to receive the package. It's technically possible, though. Retcon or just a convoluted set-up?
Conversations from the Universe mentions that other civilizations have visited Installation 04 before. However, the Anniversary terminals show that he sends out warnings and fires upon any ship within 1 light year of Installation 04 that doesn't immediately crashland.
Well, he let the Covenant get pretty damn close to Alpha Halo. Maybe he just really sucks at his job? Retcon or error?
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In addition, there are also sources from the MULTIPLAYER that should be addressed.
The multiplayer maps from Halo 2 and Halo 3 (and Halo Wars to an extent) were designed to be logical places in the Halo universe. Most of Halo: Reach's maps and all of Halo 3: ODST's Firefight maps are literally taken from the Campaign itself, securing their places in the canon. There is even a school of thought that believes the Invasion scenarios for Spire, Boneyard, and Breakpoint count as well, though it's unclear which side would canonically win.
Halo 4 takes this a step further, not only integrating the maps into the universe but also giving a canonical purpose to the multiplayer itself. The multiplayer matches themselves are canonized as simulations by Spartan IV soldiers on board the UNSC Infinity (just don't think too hard about it). These Spartans will then be sent onto missions that will make up the episodic Spartan Ops mode.
Halo 1's multiplayer maps, however, seem more focused on variety, but are considered canon as well. However, some have rather interesting descriptions.
Chiron TL34- Spartan Clone Training Complex
Spartan Clone training, eh? That sounds different.
ARMOR PERMUTATIONS also have their own descriptions. Some are more curious than others, and I'm not even talking about things like Hayabusa.
To the point, there's the following tidbits from Halo 3's descriptions:
Security Armor- The Mjolnir Mark V(m) Powered Assault Armour was originally manufactured in 2528 and recently upgraded to be compatible with all current - issue armour variants.
Wait. MJOLNIR Mark V, which was introduced to Spartan 117 in 2552 (and other Spartans in 2551) was actually manufactured as a Security variant much earlier? That doesn't sound right. Hang on, it gets worse.
UPDATE- Halo Encyclopedia changes this to the equally illogical 2543. Reach gives the same 2528 date, without the "Mark V".
Mark V- Originally issued in August 2542, all extant Mark V helmets have been upgraded with current - issue internal components and software.
Retcon or error? In terms of the Mark V's constantly changing issue date, I'd say retcon.
UPDATE: This might be an error caused by Bungie and the Encyclopedia following an incorrect date posted in later editions of FoR. Still wrong, though.
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Before I go any further, I would like to touch upon the shields on the Halo Wars Spartans. They are a great example of Gameplay and Story Segregation.