Well, I do know that milk tends to make me get thick in the back of my throat when I have phlegm (when I have/getting a cold or when it is really dry, say in the winter with the house heat) and OFTEN times I cough to try and raise it and I vomit. I would perhaps either not give him the milk before bed til he is phlegm-less, perhaps water it down a bit, or have him lay with his head elevated in the bed. Maybe he is about to get a cold, poor bub.
If he isn't having trouble with said milk any other time during the day, I would tend to think it's not the actual milk but a combo of laying and milk and coughing. Just my opinion!
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I hope it stops soon.
Zoey