When is it acceptable to have a pronoun without a clear antecedent?

Here is an example of what I'm talking about:

Dental caries and gingivitis can be exacerbated not only by what patients eat but also by when they eat it.

The bold part is the correct answer for that sentence. Clearly, it doesn't refer to anything. Logically it refers to food, but food is never mentioned.

In the MGMAT SC book, it categorically states that you can't have an unclear pronoun. Yet, here we are...