These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
YMMV: Honest Trailers
Critical Research Failure: When discussing Pacific Rim, the Narrator asks why Gipsy Danger didn't just whip out its BFS and kill Otachi and Knifehead immediately. While the point stands for Otachi, the sword hadn't been installed yet during the Knifehead fight 5 years earlier.
A minor example, as well as probably a case of Adaptation Displacement, in the X-Men trailer, where the Narrator points out how Rogue only gets "the crappy part of her powers" (her Power Parasite ability), but not the flight and super-strength she had in the first cartoon. Anyone familiar enough with the comic knows power parasite actually is the only ability her mutation grants her; the Flying Brick abilities were only something she gained by absorbing Ms. Marvel's powers, which obviously never happened in the movie franchise.
Another minor example from the same one includes mentioning that Psylocke didn't appear—expect she did appear was one of Magneto's brotherhood in X-Men: The Last Stand.
For the Star Trek Into Darkness trailer, the narrator says that Khan is "completely justified in his actions" because he's trying to rescue his family. This overlooks the fact that he orchestrated a terrorist attack on a Starfleet facility and killed several of Starfleet's high command.
Also, Admiral Marcus claims that he was plotting to Kill All Humans out of Fantastic Racism as he thinks he and his cohorts are the Master Race. When the Enterprise brings this up, Khan doesn't confirm it, but he doesn't deny it either. He plans on killing everyone on the Enterprise after he's got what he wants as well, and later crashes his ship into Starfleet Headquarters- aka San Francisco- purely out of spite, probably killing hundreds of people. So yeah, he's actually kind of a dick.
Hilarious in Hindsight: The ending of the Avatar trailer has the trailer guy saying, "Ugh, fine, we'll recycle, just make another Terminator!". While James Cameron may not be doing it, the Terminator is getting another movie (albeit a reboot).
Possibly lampshaded in the Star Trek Into Darkness trailer when Alice Eve, who plays Carol Marcus, is nicknamed "Thumbnail."
Replacement Scrappy: The current Narrator voice, Jon Bailey, sometimes gets fan complaints for not sounding quite like the previous Narrator, Gannon Nickell, who had to leave the series for military service.
Hal Rudnick: So I know a lot of you guys are big fans of the Honest Trailers, so much so that you say you wish I'd die in a fire so there'd be no more Screen Junkies Show and only Honest Trailers! Sorry! I'm still here!