What causes babies to ingest milk into their lungs?

Aspiration. The swallowing and breathing tubes use the same mouth and rely on a transitional structure called the epiglottis to close over the breathing tube and allow you to swallow food/fluids. If a baby is breathing in while the fluid is trying to go down, some can sneak passed the epiglottis and be inhaled into the lung. Luckily this rarely happens.