Maybe it's a touch of a cold or just the difference of being flat longer overnight.

I used saline drops and a bulb syringe to clear the yuckies out of Tatiana's nose when she was small.
Of course, saline drops and a bulb syringe aren't going to help with the not being wide awake at the end.

I kind of doubt that there are irritants in the bedroom. Though with the cold maybe the air is too dry for him. I wonder if saline drops before bed would keep it from happening. I think Dr. Sears tells how to mix Saline drops for infants at home in one of his books.

We always put a pillow under her mattress when she was stuffy to elevate her head but she always slept in the crib beside the bed not in our bed so I don't have anything helpful along those lines.

Teething often causes odd nose issues as well. How long has it been going on?

I hope it gets sorted soon.