A lack of understanding what we read is most clearly connected with which of the following?

It depends on the reader and how they are reading it, some people don't understand poetry, some people don't understand romance etc. Sometimes it is lack of paying attention to what they are reading or they are trying to rush through the reading instead of the student being able to read at their own pace.

Are there choices?

well one way is associated with reading the text and not understanding or paying attention to what you are saying.