Schedule Slip: When the series was covering Ocarina of Time, episodes only took a couple months at the most to be released. But when Majora's Mask Abridged began, the episodes gradually started taking longer and longer to release (with several videos lampshading and discussing this), with a mind-boggling six years between episodes 13 and 14.
xanauzumaki's series:
Real Life Writes the Plot: Which could explain why the opening conversation in episode 13 of Twilight Princess Abridged revolves around nothing but wisdom teeth.
Throw It In!: Several examples, though the biggest one is probably Midna mistakenly calling the Mirror Shards "Fused Shadows" in an episode. It eventually turned into a Running Gag.
