1. Causes of Babies’ Breathing Shortness of Breathing in babies is a common symptom that may be caused by many reasons. Here are some possible causes of wheezing in babies: 1. Respiratory infections: Respiratory infections are one of the most common causes of breathing difficulties and wheezing in babies. This infection can cause symptoms such as nasal congestion, cough, sore throat, and fever. 2. Bronchial asthma