Occasionally, the player's Pokémon wil ltake a rest from Core Training, indicated by the Pokémon lying on its side with a "…" displayed above it and a refusal to participate in a Super-Training Regimen (or accept a new training bag); tapping the Pokémon will wake it upand give it a second wind (shown as a smiley above the Pokémon), which doubles the speed at which the Pokémon can finish off a training bag. ~ Bulbapedia
A Pokémon will be neutral most of the time. It will fall asleep if you it sits idle for too long, and occasionally in between Training Bags. It will wake up once you tap it, become "refreshed" and defeat the first Training Bag you give in half the time. A Pokémon that is KOd will not wake up if you tap on it and will only wake up once it has been revived.
Sources: Bulbapedia and Personal Experience.