Ascended Fanon: Of the premeditative variety. When the counter debuted in Episode 13, viewers calculated that, if it counted down in real-time, it would reach 0 on April 23, 2012. The writers made it so that Episode 16, wherein the counter activates, would correlate with that date, though because Keroro makes the counter activate a week early, the episode was uploaded a week earlier as well.
The creators openly disowned the original Episode 1. They remade SFA1 to make it funnier, more in-line with their current writing style, and to make it in-canon with the current continuity. They don't think very fondly of Episode 2R either, and they remade it as well.
They refer to the original first two episodes as "SFA1R" and "SFA2R", the "R" standing for "Retconned".
Thorn is also fairly unhappy with Episodes 8 and 13. Not enough to retcon and remake them, obviously (though as of reviving the series, they're not off-limits anymore).
For a time, Thorn kept forgetting that Tamama was male and not female; after coming up with a joke that would reveal that Tamama really was a girl, he and Yoshi decided to make it canon. After deciding this, they would occasionally make unintentional Freudian slips revealing this, but they simply pretended that they were still confused about Tamama's gender. Then Episode 10 rolls around...
Giroro, Kululu, Mois, and HQ all had voice actor change-ups after their characters had already appeared (to say nothing of the numerous voice actors hired to voice Dororo, Momoka, Omiyo, and Natsumi but were removed before they ever appeared in an episode).
There was supposed to be a running joke involving Thorn and Yoshi trading off each episode as the voice of Tamama, but Yoshi only voiced the character in Episode 3R before retiring as the second voice. It was one of the reasons that Episode 3 was remade despite being a mostly competent episode.
Momoka was voiced by LillyLivers for her debut in 2R, but was voiced by Narusasu in Episode 10 onward. Narusasu would also do Momoka for the Episode 2 remake.
Lampshade Hanging: Giroro's voice change is joked about in the Episode 3R stinger as him getting over laryngitis and losing 300 excess pounds. Kululu says a similar thing in Episode 10 by saying his voice change was him getting over a chest cold.
The Other Marty: ThePS2God, the original voice of Momoka, Omiyo and Dororo, had recorded lines for Episode 2(R) before being kicked from the project. However the then-script ended up not fitting the source video, so his recordings were scrapped.
Lil' Keroro's over-the-top la-la-laing in Episode 4 was just Yoshi goofing off during recording. Thorn wanted to keep it, and it was even brought back in Episode 7.
Also Lil' Keroro's shocked expression in Episode 4 is simply a frame of him turning his head that Yoshi discovered by accident.
Keroro brushing his toothbrush in the Episode 2 Post-Credits was a result of Yoshi mistyping "I'm going to brush my teeth" as "I'm going to brush brush my toothbrush" during scriptwriting for SFA2R. Thorn liked the idea of Keroro brushing his toothbrush, so it stayed. It was edited for 2R, but the entire line was later put into the remake.
Keroro's comments to Dororo at the end of Episode 14 - about remembering his name and giving a high-five - were ad libs by Yoshi.
Keroro trips over himself trying to say a tongue twister in Episode 16. Yoshi was supposed to joke-flub the line; the take used was him messing up for real.
Travis jokingly did a parody of the THX crescendo while doing the monster powering-up yell in Episode 18. This ended up being the take Thorn used in the episode.
Un-Canceled: Originally ended November 2012, with the creators seeming prepared to never look back. Three months later, Thorn was more than happy to bring it back and do it again.
There was talk briefly during the series' early days of it becoming part of WingerDinger Productions, due to LillyLivers' association with the project. This was shortly before WingerDinger was hacked and subsequently abandoned, so nothing became of it.
The writers intended to bring back Momoka after killing her off in Episode 13, but her voice actress Narusasu moved to Japan shortly after the episode went up. As a result, they simply left her dead.
Wafer Thin Mint: On the subject of Momoka, she had several voice actors (and people contacted about voicing her that never made it in) before her first appearance in Episode 2R (at the time voiced by LillyLivers as a backup). The constant trouble the team had getting her a voice is the reason they didn't simply look for a new VA after Episode 13, effectively being the final straw that broke her character's existence.
In an even stranger example, the climax to Episode 10 with Future Kululu is what happens when Thorn takes numerous disparate elements from the first season and decides to tie them together. He and Yoshi barely planned for the climax prior to scriptwriting, and Episode 10 in fact had the most planning of any episode up to that point.
Viper only became Dororo's father when Yoshi joked about Viper's eyepatch being similar to Lil' Zeroro's mask. They just ran with it.
Happened again when writing for Keroro's monologue in Episode 18. The intention was for him to blame his parents for all the troubles in his life; after two minutes of thought, it turned into a reveal that Keroro is Dororo's little brother.
Written By Cast Member: Thorn and Yoshi are the writers and lead voice actors. Episode 6 was co-written with Natsumi's VA LillyLivers, and Travis voiced various minor characters before becoming a recurring co-writer with Episode 9.
Yoshi never intended to be a voice actor, let alone the voice of the main character; he just wanted to script-write and oversee the project. While he didn't quite like voice acting during the first three episodes, he began enjoying it starting with Episode 4, and it became one of his main hobbies after stepping down as SFA's writer.
Thorn admits that he wanted to run the project and voice practically everyone in the formative, circa-SFA1R days. Fast-forward to 2013, and he does run the project and voice a majority of the cast.