Well, a lot of it has to do with pumpkaboo’s nocturnal nature. They’re most active at night, which means their 2 to 4 am is your 2 to 4 pm. As such, they simply get bored, especially if you’re not awake to give them affection. For this reason, some pumpkaboo owners like to give their pokémon plenty of toys—especially complex ones or sturdy ones that can endure heavy use—to keep their pumpkaboo occupied until they’re awake. Given that yours is sitting on your chest, waiting for you to wake up, I have no doubt it’s just that your pumpkaboo needs more stimulation during her most active hours, and this may be your solution.
Alternatively, wild pumpkaboo take it upon themselves to lead lost souls to the spirit world. In Kalos, they’re even considered an equivalent to the Grim Reaper. This, of course, shouldn’t be any cause of alarm. Rather, what I’m saying is that your pumpkaboo may also be worried that you’ve died, and it’s observing you breathe as you sleep while watching your spirit. You can reassure her that you’ll wake up in the morning by establishing a routine with her: wishing her good night every night, then wishing her good morning at a set time every day, just before feeding her breakfast. If she gets used to such a routine, she’ll come to rely on its dependency, rather than on her own observations, which will allow her to leave you alone at night.
I would recommend doing both (giving her toys and establishing a routine), as it can’t hurt to do both at once, and, if anything, it will be more of a comfort to her.
Best of luck, anonymous.
The Pokédex According to Bill 