Spouse Retirement Tax Rate

My husband retired last year and has a pension. He had taxes taken out of his monthly pension check. I am still employed. I am noticing that when adding his 1099-R he is taxed at a very high rate. Why is this? What is the rule about married filing jointly that requires his pension to be taxed at such a high rate? Should we file separately or will this trigger an audit given that we have been married for 30+ years and have always filed jontly? What do married couples do when this happens?