They are an indication of what is missing in your presentation. They come in 2 types:

• Easy ones. You think something is so blatantly obvious that you saved some slides by taking it out. Apparently your audience disagrees. 

• Hard ones. If everyone brings up this question, and you know it is one of the weaker point of your story, you might as well address things, since even if you had a meeting where the question was not asked for a change, it is highly likely that the audience did still have it.

Read your audience carefully. Does the same person ask the same sort of question again after she said that she understood a previous answer you gave? Does the person say she understands, but her eyes tell a different story