When I was a kid I used to think I was allergic to getting up in the morning, because I would always wake up with a stuffed up nose and a slight cough. It happened so often that I think my parents thought I was always just trying to get out of school (admittedly, I did try to get out of school fairly often).
It's only as an adult that I've realized that I have dust allergies and those symptoms were probably because I was just really bad at making sure my room was properly vacuumed.
I didn't spend much time in my room except to sleep, so it was no wonder that I never felt ill at any time except in the mornings. I wish I had known it back then because it was slight, but it was extremely irritating and it made getting up in the mornings that much worse.