The Other Darrin: Just for one episode (Episode 9). Since Cipher/TJHerriot (Reiji and Nico Smiley's VA) was not around to record for that episode, wraith10 and Tyrest voiced Nico and Reiji respectively.
Screwed by the Network: As of Jan 2017, the channel was taken down 2 times on Youtube. Nothing new right? They even lost their channel on Dailymotion. Uploading the episodes is going to be so much harder
Talking to Himself: Happens often. Special mention to Mana, who voices at least ten characters.
Throw It In!: According to the commentaries, some of the lines that are ad-libbed by the voice actors when they were recording their lines.
Azzy mentions that the opening disclaimer would be different every episode in second episode commentary.
Azzy and Mana mentioned that they have the other lines for the "I'M FAIRLY PASSIBLE" scene of Episode 1 that references to both the original and the abridged series of Yu-Gi-Oh! but decided against it.
In fourth episode commentary, Mana mentions that they could have added a line for Astral in his cameo with Yuma but Tyrest was not available to record a line.
Tyrest (VA for Michio and Shingo) says that Michio's accent was supposed to be more like Mario's but he softened it because he wanted a more appropriate voice for him in the Cast Q&A.
Azzy mentions in the commentary of Episode 7 that Shun would have a completely different characterization. It changed when Shun's VA did some random screams in their first recording session and Azzy decided to add his screams to the series.
Atra Voce (who voiced Kyuando Eita) was going to voice Jean-Michel Roger but was not able to due to some conflicts. Roger is now voiced by CoffinJockey.
The commentary of a reaction video of episode 21 has Azzy state that he did approach BlazingAzureCrow to voice Yusei, but he declined.