- Executive Meddling: The entire premise of the series. Dan Didio absolutely hated 52 because DC's editors had little to no say in how the series unfolded. Countdown was conceived as "52 done right" by Didio as a weekly series where DC's editors had ultimate control over every single issue. Fans didn't agree with his sentiments and the results was a hodgepodge mess of a story that had little to no coherency. This resulted in a real life All for Nothing as Final Crisis didn't even allude to this series let alone follow any of its storylines.
- For that matter, the appearance of the New Gods - Grant Morrison wanted DC to minimize, if not outright refrain from, using them, so when they did reappear during Final Crisis, their impact would be much bigger. Either DC ignored their request or didn't get it, and regardless of which was the case, they opted to do the inverse and have them appear everywhere - this series, Death of the New Gods, and Amazons Attack!.
- Screwed by the Lawyers: Why does Superboy-Prime show up as Superman Prime (No, not that one)? DC had lost the Superboy trademark to the Siegel family around the time of Infinite Crisis; while they were able to use the regular Superboy for that event to kill the character off until they got the rights back, since Prime was still around after the aforementioned Infinite Crisis, their options were either not use him at all, or rename him and give him a Plot-Relevant Age-Up. They ultimately wound up choosing the latter, although as soon as they got the Superboy trademark back, they undid said age up and changed his name back.
Trivia / Countdown to Final Crisis