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.
Alternate Character Interpretation: The theory has been made that her power is actually the ability to warp reality. This is why she is able to defeat such strong opponents; the "talking to squirrels" shtick is just what she chooses to live as.
Some people even think that she might be an Aspect/Avatar/Personification of The One-Above-All himself, who occasionally comes to Earth to have a little fun.
Author's Saving Throw by way of Worf Had the Flu: Uatu the Watcher is present in the panel where Squirrel Girl had defeated Thanos just to clarify that that Thanos isn't a "robot, clone, or simulacrum". Then in another series, Thanos mentions that he can create clones of himself that even the Watcher cannot tell aren't him. And thenWord of God states that that Thanos really wasn't a clone. All these were written by Dan Slott, making him pingpong against himself. It's not the first time he's has gone back and forth like that. Just look at the whole She-Hulk/Juggernaut thing.
Broken Base: Squirrel Girl's slightly chubbierredesign for her solo series. Some think she's still adorable, but others think the design choices made is a rather ill fit for her. There are also some who are disappointed that the rest of the Great Lakes Avengers are getting the shaft in favor of Squirrel Girl.
Fanon: Somehow people are convinced that the weaker the enemies, the more likely Squirrel Girl is to lose. (Tell that to the Bug-Eyed Voice and those muggers in Central Park.) This is only going to get worse now that she's been "defeated" by a baby.
Although, given the line of dialogue that suggests that, Wolverine saying "I thought we agreed never to see each other again," it may be more about Wolverine wanting to save face than indicative of a past fling.
Some people wouldn't be nearly so aggravated over all the "Squirrel Girl is awesome and can beat everybody" talk if it weren't repeated so constantly by so many of her fans.
There's also the fact that her explosive popularity means Marvel is starting to place her in other titles as well, though not to quite the same extent as Deadpool... yet. The fact that she apparently maintains her Plot Armor and ability to completely school more serious, more powerful, and more experienced superheroes outside of the comedy comics she was usually in is starting to generate even more backlash, considering it means she's transforming from a Parody Sue to just a plain Mary Sue.
Internet Backdraft: Any Squirrel Girl thread has the potential to blow up into a fight between people who think that anyone who would dare to take a comic seriously is an idiot and that superhero comics should be as goofy, carefree, and lighthearted as possible, and people who think the term "funny pages" should not apply to their Graphic Novels in any way, shape, or form and that the goofy bastards are seeking escapism without angst.
The art style for the "Unbeatable Squirrel Girl" comic has met with this.
Marvels website lets contrasts the power levels the fans believe a character to be at with the power levels they are officially at. And its the official power levels that are through the roof (topping every single field), so Marvel thinks she's even moreBadass than even her fans do!
Memetic Mutation: The whole reason she ever reappeared was because her introductory appearance became a meme.
Over Used Running Gag: Some people feel that the "Squirrel Girl beats everyone" joke is overdone and wish that there would be at least a few moderately serious stories about her so she's defined in some other way than "goofy character who can beat up Dr. Doom".