Sometimes students feel baffled by a reading assignment and express that frustration in class, but they often understand more about the reading than they believe they do. When this situation arises, having students write about the reading can be especially valuable, both for clarifying what students do and don't understand and for focusing students' attention on key points in the reading.
If you know a particular reading assignment is likely to give students trouble, you might plan questions in advance. But even if students' frustration catches you by surprise, you can easily ask questions about the key issues or points in the article. Moreover, asking students to answer the same questions again at the end of the class, after you've had a chance to discuss the reading, will help you see what students still don't understand.