While the story hasn't be declared yet, Discorded Celestia: Not Loved gave Discord the middle name Apophis and last name Typhon. "Different From Everypony Else" had this made his official full name. Also both a bit of Genius Bonus and Nightmare Fuel to fans of mythology who know just what those names mean.
This piece of fanart (a sequel to a certain scene in Dark World) was eventually inserted into the fic.
Alexwarlorn noted that despite describing Pandora with a fox's tail, fanart kept showing her with a lion's tail instead. Eventually, he had Discord comment that Pandora went through a phase where she replaced her lion tail with a fox's for a while before going back.
The Nameless Passenger in Dark World is eventually revealed to be an evolution of Nightmare Purgatory from the "Fading Futures" Recursive Fanfiction.
Ascended Meme: Cutie Mark Failure Insanity Syndrome gets a shout out in Shining Armor's 10th chapter.
Creative Differences: Seems to be a genuine case between Alexwarlorn and LZ0291 given their comments, as a number of their arguments seem centered around the directions the fanfic goes in. While neither sides have parted ways, LZ has come close on a number of occasions and the two fight from time to time in the comments.
The fighting between the two eventually got to the point Godzillawolf left the project altogether rather than be between his friends.
And now it's gotten to the point that the disagreements between the two has practically turned into hate and the two's grudge is threatening the story as a whole.
Creator Breakdown: Alexwarlorn has had several over the course of the story, though thankfully he's managed to recover each time and it hasn't effected the story much.
LZ0291, the writer of the Shining Armor arc, suffered one, feeling that no one cared about his arc and was seriously considering quitting the project. Fortunately, the fans let him know that they did care, and he recovered. It was later revealed this was in part due to clinical depression.
Godzillawolf has also had minor one due to Real Life events (including the death of a family member) putting tremendous stress on him combined with various Troubled Production related issues. He managed to recover, thankfully, and the story wasn't effected.
I Knew It: At least a few people called The Reveal that the Interviewers were born from Amicita and essentially created Shining Armormonths in advance. One particular fan sent private messages to both of the main authors saying that he had figured it out a year before it was officially revealed, and was specifically told by both of them not to share it with anyone.
That same fan figured out that Cobweb was Trixie the moment she appeared.
Promoted Fanboy: Kendell2 started out as simply a fan, then became a beta reader before actually getting to write some scenes a finally even threechapters, including a Shining Armor arc chapter written to supplied notes, and co-writing the chapters from 14 onwards. He refers to himself as this trope in the description. He also wrote the original lyrics for the original Reharmonized audio adaptation's theme song, though they were altered somewhat for the final version.
Troubled Production: Due to the sheer side and scope of this fic, combined with issues in outsourcing for the G2 Dreams/Nightmares arc, this fic has been in quite the rocky situations.
And by this point, Louis (producer of the Audio Adaptation and one of the main editors for the fanfic) is the only person on the main crew that hasn't had a Creator Breakdown at some point.
Alexwarlorn and LZ's relationship has also become strained, leading to disagreements between the two that ultimately caused the SA arc to be frozen in Development Hell for a time. On top of this, LZ developed clinical depression at some point in production (part of or the reason for the fighting) and the fighting between the two lead to Godzillawolf departing from the project. Thankfully, the two were finally able to make amends enough to finish the SA Arc together so they could both finally move on.
And then the wedding started and the feud erupted again, resulting in LZ trying to have his contributions to the story removed. It seems the two of them just can't seem to put their grudge behind them and move on.
Louis also seems to have vanished as well but returned in time to help some with the final chapter of the SA Arc.
Alexwarlorn wasn't originally supposed to write any of the 7 Dreams/Nightmares chapters, but ultimately had to write Bright Eyes' story due to losing contact with the original writer.
Chapter 36 of Dark World originally had scenes of Amicita restoring Neo Stream to existence and healing/redeeming the Emperor of Man. However, complaints from Neo Stream's owner in the former case and pressure from critics in the latter case forced Alexwarlorn to remove both scenes.
According to Word of God, Makarov was originally only going to be in the SA arc for half a chapter, but somehow spun out to be Big Bad of a whole saga. Reviewers have commented that he seems to have done his job as a ParodyBlack Hole Sue a little too well.
Actually, it's a little more complicated. The original original idea was a regular parody sue existing for half a chapter... that became Makarov. Bugger.