Executive Meddling: According to reports, this happened to Episodes 11 and 12. Apparently, Episode 11 was too long to air, so the first part of the episode was replaced by a Clip Show. The second part of Episode 11 and the first part of Episode 12 make up what was originally intended to be Episode 11, while the second part of Episode 12 was supposed to be the episode's first part. Meanwhile, the actual second half of episode 12 was cut, leading to the Gainax Ending. There's also word that there was trouble completing the animation deadlines for some of the material. The Blu-Ray release includes a special director's cut version of episode 12, restoring the cut material.
Which unfortunately didn't make it over for the US release, as Sentai was given the broadcast version to work with.
Fandom Nod: In Episode 3, Joe says that his team is pathetic compared to the previous Gatchamans.
What Could Have Been: The artbook for the series revealed that O.D.'s design was originally meant to be for Berg Katze, but eventually became used for another Gatchaman team member as it was decided he'd work better as a friendly type. In addition, Joe was originally to be a more wild and mischievous type of character, and initial drafts had him with red eyes and a black jumpsuit. It is also said that his hair was initially to be shorter, but it was decided that Sugane would have the shorter hairstyle instead. Utsutsu was originally designed with the feel of a "tough-natured, sexy" type of girl, but she became the shy and withdrawn type.
Hajime herself was originally going to be "G-6", and the suits initially looked more like armored versions of the Birdstyles from the original series. Sugane was also to be the main character, but it was felt that Hajime's personality worked better for the lead role.