Alas, Poor Scrappy: The gang's treatment of Duck and Ben have been seen as too cruel, to the point that even people that hate them are sympathetic.
Alternative Character Interpretation: Their movie night screening of A Talking Cat!?! features them providing one of these for every single character in the film. Susan is an unstable drunk; her entire family want to have sex with each other; Phil is senile; Chris pretends to be awkward at romance in order to get with everyone; and Duffy does everything purely because he likes watching young boys in swimming pools. Please note that A Talking Cat is supposed to be a kids film.
Archive Panic: Just look at how many games they've covered. Good luck watching them all.
Broken Base: Making people pay to chat in their stream chat was quite the base breaker years ago. Some people have dealt with it, and others have sworn to never watch their content ever again despite the fact it is a $50 lifetime fee to do so. The reason why they did so was to prevent trolls and such from ruining the experience.
Complaints came in by the truckload when the show started to get Minecraft-heavy (even though Fraser has never abandoned or substantially reduced non-Minecraft content), though many fans now consider these shows to be a VGA staple.
Complaints also poured in when Fraser, Ben, and Becky started a fullscreen Long Haul of Borderlands 2 that was much more similar to a normal Let's Play than the usual show and lacked a visible chat. These complaints increased due to the fact that these shows began in October and were taking the place of many promised spooky games and because of the increasing levels of grumpiness and frustration Fraser was showing on the normal shows, which some blamed on having to be taken away from the much easier to produce Borderlands episodes. Of course, many people adored the episodes because of their relaxed atmosphere, the co-op dynamic, the game itself, and the unique experience of getting to watch Becky learn how to play an FPS.
There are also fans who prefer the recorded 5 to 15-minute shows to the live multi-hour shows, or just want more episodes of Awesome Video Games. The "abridged" episodes have since been reintroduced to satisfy those who desire shorter shows.
There are also those who show incredible bile towards the gang (Fraser especially) for putting forth little effort in understanding the plot of some games, misinterpreting important aspects or features, blaming the game for their own mistakes or lack of attention to instructions, or offering incredibly inconsistent criticism from game-to-game. The other half of the fandom see this as the best part of the show, as it provides plenty of opportunities for humor and gives the show a much more casual atmosphere.
The Silent Hill 2 playthrough was perhaps the biggest controversy in the shows history so far, largely because of ignoring the plot (see above) and unfavourable comparisons to Deadly Premonition (which the team were much more invested in). However, some viewers agreed with much of the gang's criticism and/or saw the massive protests against the gang's mocking of the game as simple fanboyism.
Crosses the Line Twice: During their Heavy Rain Playthrough, Becky comments her dislike of the word Corpse Fucker, the boys respond thusly
Fraser: Remember Becky? If you bring that you don't like something, we'll beat it like a dead horse.
Ben: And then we'll fuck it.
Ear Worm: Fraser's impromptu sea shanty in Minecraft Survival episode 49 (at 29:22). Saaaailing, across the ocean blue...
Near the end of Fraser's vlog on June 10, 2011, the rest of the gang comes into his home with beer for the hockey game. At about 7:36, With Fraser still talking, Ben comes up from behind him and kisses him on the ear.
Ben takes a lot of opportunities to playfully flirt with Fraser (like in their liveshow of Earthbound) and touch him (reaching into his lap when playing Halo: Reach, in the You Don't Know Jack episode when he first comes back), which Fraser seems strangely used too. With Deacon too, In the NHL 2011 Playoff game Deacon and Ben were dancing quite closely. They also tend to hug each other a lot as well. And again in the Pre Minecon Minecraft Show.
Deacon tried to kiss Ben in the Pre Three post show.
Then there's the bit where Fraser mock-serenades Ben with a violin in Wii Music.
While playing The Walking Dead, Duck and Ben are treated with absolute loathing by the gang due to how useless, cruel, or incompetent they are. Fraser continually makes all of his choices based on getting them killed, even though both of them are kids. By the time Duck dies, he's come to peace with him due to how crappy his situation has gotten. He outright murders Ben, though. Considering how Ben is indirectly responsible for Duck's death, Katjaa's death, and the near-death of several others, some may have felt this justified.
In Phoenix Wright: Ace Attorney, even though they love most of the characters, even the villains, Fraser shows contempt for Angel Starr for being so spiteful against everyone, and Lana Skye for being so adamant about not helping Wright defend her. Fraser also lost it in regards to Acro, mostly because the game was trying to still painting him as sympathetic after he admitted to wanting to kill a little girl and only killed someone else by mistake. Moe the Clown was likewise despised for being too much of a pain.
This is Fraser's reaction towards the end of the BioShock Infinite playthrough, when he finds out that Elizabeth, who he has been jokingly lusting after the whole game is the PC's daughter.
The whole gang (especially Fraser) reacts in horror when they learn while playing Fibbage that there's a Chinese dish that involves cooking eggs in young boy urine.
"Stop Having Fun" Guys: Mostly averted, as the point of the show is to depict friends having fun with video games. There are some members of the Chat who play this straight, at the risk of being trolled by Fraser and company.
The overwhelming mediocrity of 1-2-Switch took a visible toll on both Fraser and the chat (by the end of the episode, both parties were begging for it to end). They later did an encore episode in which Kyle, Deacon, and Ben (who were absent for the initial show) got to experience the pain themselves.
Superlative Dubbing: Fraser, being a Man of a Thousand Voices, likes to dub over the character's lines in games where there are no voiced dialogue. Sometimes this goes surprisingly well. Especially evident when they LP the Phoenix Wright games.
The Woobie: Ben. A doctor advised his mother not to give birth to him. Fraser constantly brings up his dyslexia. An old man in a park offered him drugs in exchange for blowjobs.