Hypoxemia, or low blood oxygen, can be caused by any of the following medical problems: anemia, airway obstruction, congenital heart disease, chronic obstructive pulmonary disease, emphysema, high altitudes, pneumonia, pneumothorax, pulmonary edema, pulmonary embolism, pulmonary fibrosis, shock, or sleep apnea.ypoxemia, or low blood oxygen, can be caused by any of the following medical problems: anemia, airway obstruction, congenital heart disease, chronic obstructive pulmonary disease, emphysema, high altitudes, pneumonia, pneumothorax, pulmonary edema, pulmonary embolism, pulmonary fibrosis, shock, or sleep apnea.