Some of the limitations of applying feminist theory to a text are the same limitations that arise from applying any theory to a text.  When we apply a theory to a text, we are viewing it through one lens, one perspective.  This constricts our ability to see any other perspective as we critique a text, much as if we applied only Marxist theory or used Freudian or Jungian theory in our reading.  We filter out any ideas or meaning that might be otherwise present.  Essentially, this is selective perception, which opens our minds in only one way and closes it in all others. This is not to say that any of these are not legitimate perspectives, but to say that as one critiques text using one perspective, one should have an awareness that there are other legitimate perspectives to use.  One interesting exercise is to find a text and apply several different kinds of literary analysis to it, which will allow you to see a text in multiple perspectives.

Another difficulty I see with feminist theory in particular is that some feminist schools of thought operate on the premise that male and female are purely social constructs.  To the degree this is correct, feminist theory has some utility as one considers a text.  But as we gain more knowledge of nature versus nurture, we are learning that it is not really nature versus nurture at all, much more something like nature plus nurture, now called epigenetics, which suggests that biology is more important than we think it is. If that is the case, feminist theory, which is really a form of political theory, has some re-thinking to do.   

There is one main limitation of Feminist Theory when applying it to a text.

The problem with Feminist Theory is that it typically the subject depicted in the text is rooted in social and cultural spheres. Instead of looking at the individual (in regards to how they fit into society and how others look at them), the texts normally examines the society the characters live within.

In order to use Feminist Theory, one must (generally) examine how a character is treated within a patriarchal society and the oppressive nature of the society around the character. Another problem that arises from this is the fact that the traditions and culture of the society is examined in regards to the individual character. The problem here is that in many cultures and societies, the role of the male has been superior to the role of the female throughout time. In a society like this, it is very hard to separate the individual from the society they live in.