I don't believe that Alcott is arguing against Transcendentalism, per se, but rather she is taking issue with the men in her "utopian" community who prefer to focus on philosophy at the expense of survival. They seem to want to sit around philosophizing all day rather than doing the hard work required by the Massachusetts land to keep people's bodies alive. It isn't enough to merely sustain one's mind or one's soul: people need to eat. Herein lies the moral of Alcott's fable.

The narrator says that most of the men "were so busy discussing and defining great duties that they forgot to perform the small ones." This kind of behavior is certainly not part of Transcendentalism—Henry Thoreau and Waldo Emerson, for example, did not make the same kind of egregious mistakes that the men at Fruitlands made. Thoreau, in fact, tended his own garden (and ate the animals he caught), believing that this kind of work—making the earth say "beans" instead of "grass," as he put it—was so important to the individual who wishes to become truly self-reliant. Transcendentalism isn't just philosophy, it's about a philosophy that underwrites a particular kind of hard-working lifestyle. Therefore, Alcott seems to be taking issue with the Fruitlands' men's high-minded idealism (that looks a lot like laziness) rather than Transcendentalism.

Alcott's short story "Transcendental Wild Oats" is based on the time she spent with her family in a Transcendental community called Fruitlands in Harvard, Massachusetts. She described her experiences as a fable, or a story that has a moral, because it conveyed the impracticality and gender inequality of the utopian living that the Transcendental movement envisioned. 

Rather than using her family's real names, she refers to them in the story (written many years after her experiences in the 1840s) with pseudonyms. For example, her father, Bronson Alcott, is referred to as "Abel Lamb," and the other characters have allegorical names such as "Sister Hope." The male heads of the farm, Abel Lamb and Timon Lion (Lion represented the real-life Charles Lamb), start the Transcendental community with idealistic hopes that they describe in the following way:

No milk, butter, cheese, tea, or meat appeared. Even salt was considered a useless luxury and spice entirely forbidden by these lovers of Spartan simplicity. A ten years' experience of vegetarian vagaries had been good training for this new freak, and her sense of the ludicrous supported her through many trying scenes.

In other words, while the men are concentrating on philosophy, the women are forced to deal the reality of how hard it is to provide for themselves. The men, called to Transcendental abstractions, do not even harvest the grain. As Alcott writes, "About the time the grain was ready to house, some call of the Oversoul wafted all the men away."

In the end, the community, faced with a harsh New England winter, must abandon the farm. Alcott seems to be arguing against Transcendentalism, particularly its impracticality and inherent sexism. While the men in the community are committed to building an ideal society, they don't carry out the practical tasks necessary to sustain their lives. Instead, the men make their families shoulder the burden, and everyone must leave the community when they realize it cannot sustain itself.