Creator Backlash: None of the people who worked on the Jaffa Factory series are really fond of the bee breeding and power supply part of it. In part 7 of MoonQuest, Simon explicitly says that once the Jaffa Cakes started being shipped onto the truck, the series after that got "really boring". They've said that if they can find a way to breathe life back into the series and freshen it up, they will, but tell us not to hold our breath.
Mean Character, Nice Actor: It is important to note the difference between the Yogscast members themselves and the characters they play in the Tekkit series. Whilst they are to some extent playing As Themselves, there are some major changes made in order to facilitate the story. For example, there is no fierce rivalry between any members of the Yogscast. They're all friends with each other, and any "rivalries" are lighthearted and entirely for fun (or in Rythian's series, as part of his Tekkit story).
Series Hiatus: The Shadow of Israphel. When the series seemed to abruptly stop putting out new episodes in the middle of season three, there were/was/is lots of speculation that it had become an Orphaned Series. Lewis has said that it simply can't be continued at the moment because of real life constraints and some of the original crew not being around anymore (not that it stopped complaining about SOI's hiatus or speculation he was lying). Every once in awhile they throw in a Shout-Out in some of their other series alluding to/joking about SOI taking so long/being constantly delayed.
Going hand-in-hand with going Off the Rails. Mr. Astley, for example, was not intended to be a creeper; the creeper had just randomly spawned in the dark basement that was meant to store the redstone mechanisms to play a noteblock rickroll as a door trigger that was never finished.
According to a Q&A with Rythian, Teep the Dinosaur was originally going to just run around and be an Easter Egg/Freeze-Frame Bonus during Rythian's Tekkit series. Then Teep killed Zoey on accident in a million-to-one chance, and from there they just decided to incorporate him into the story.
Duncan's constant giggling during his conversation with Rythian was because he couldn't stay in character, but Rythian liked how it ended up making him look like a mad scientist.
According to the wikia, Sjin and Sips tried getting Simon and Lewis' old guild member Yohi to join Sipsco, but he was away and Rythian ended up joining as an extra member of staff for their series.
The original lyrics for "Big Girl" were, according to Lewis on the 2013 Dwarven Dairy Livestream, much more offensive towards fat people than the guys deemed appropriate, and they had to get Sips to tone them down. Of course, given the internet, this may well have been for the best.
Why Fandom Can't Have Nice Things: It was ultimately inevitable considered the copious amounts of Fan Dumb, but as of June 15th 2013, the comments section on the main channel have been shut off. Old videos don't seem to have been affected however. As of the end of August, they seem to have come back.
Though, ironically the Fan Dumb itself wasn't really to blame, apparently the final straw was people impersonating the Blue Xephos channel flag to steal people's personal information.