My husband was told he is hypoxic following his pneumonia. What could might cause this hypoxia?

Depends. If your husband is still hypoxic after being discharged, i would believe that he is on home oxygen (i hope). Nevertheless, if he is still hypoxic, i could mean that his lungs are still in the process of healing and clearing out the pneumonia or that he has sustained damage (scarring) and that affected part of his lung(s) is not able to exchange gases (o2 and co2) anymore.