When 3 month old wakes up in the morning he always coughs once or twice but that's it for the day.been like this for weeks. what causes this?

Secretions: When infants lay on their backs to sleep (as they should to avoid SIDS), fluids from the stomach, mouth or nose can pool in the back of the throat. Transient coughing and/or nasal congestion after sleeping is often a sign of this, and more common in those with acid reflux. Since this can make them more prone to ear infections, elevating the head of the bed can help prevent it.

Normal mucous: There is always a little mucous accumulation that occurs at night from normal nasal drainage, mouth secretions. It tends to accumulate at night in back of throat while baby lies on back, as he should to prevent SIDS. Completely normal for him to clear it out upon wakening with a few coughs. Sometimes it helps to raise head of crib just a bit so baby not entirely flat during sleep.