Missing Episode: The Avengers vs. The Dark Knight Rises Part 2 was never shown because of the tragic shooting during The Dark Knight Rises premier.
The Other Darrin: Lampshaded by Batman and other characters who demand to know why Rhodey looks different in the second Iron Man film.
Real-life version: Starting from the Thanksgiving video, Random Guy's sister provided the voice of Batgirl (as it was revealed him and his girlfriend broke up), there is no information on who'll be voicing the female characters in the future.
The Other Action Figure: The Iron Man action figure used in the 2007 videos was replaced with the one licensed to the 2008 movie.
The convention videos use alternate Spider-Man action figures, as the regular movie-based figures aren't allowed due to orders from Marvel. The viewers are always confused.
This trope was also discussed in several videos.
And then there's the part in After Hours when Superman and Batman are arguing with each other, they then switch between that, and their Super Friends action figures, where they then proceed to be kind, and sweet and nice to each other. It's rather sickening, to be honest.
The Thing figure in the "Fantastic Four Quickie" differs from the one that made token appearances in later videos.
Schedule Slip: Zero Hour started in 2009. The finale (episode 7) finally debuted in 2013.
He's gotten into the habit of not posting videos for several weeks / months, then releasing a video that says new videos are coming soon. Cue several more weeks / months of waiting until he finally releases one video. Rinse and repeat. This trend really started to happen around 2011 / 2012, so its been going on for a while by now.