I've been asking this of doctors for the past couple of years. The latest, an ear, nose and throat (ENT) specialist, said the phlegm is likely from one of two causes -- or both -- that I may not be aware I have. The first is sleep apnea (where you stop breathing off and on through the night); the second is acid reflux. I starting taking prescription medicine (Nexium) to reduce the reflex (even though I had noticed no symptoms of having it), which HAS reduced the frequency of the morning coughing and phlegm from 3-4 days per week to 1-2 times per week. I'm still waiting for a sleep apnea test but I don't think I have that problem either. I've also tried nasal cleaning using a Netti pot with no improvement, monitoring my food intake for triggers, had an allergy test (all clear), so although Nexium has diminished the problem a bit, I still have found no complete solution to this annoying problem. However, others should have all these tests -- especially for Allergies and Asthma and acid reflux.
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There are a few reasons why you have phlegm in the morning. The most common is from allergies and respiratory infections. Another issue could be from asthma.