In a vacuum, the moment the bottle leaves your hand it will be in free-fall, and both the pills and the bottle will be subject to exactly the same acceleration - namely, $9.8\ \text{m/s}^2$ toward the floor. As a result, they will move together.
On the other hand, in real life there will be a small amount of air resistance which acts on the bottle (because the air in the room is stationary) but not the pills (because the air trapped in the bottle is moving with the same speed as the pills/bottle are when they leave your hand). As a result, at the moment the bottle leaves your hand the downward acceleration of the bottle will be slightly more than it would be in vacuum, and therefore slightly more than the pills, so the pills will begin to rise very slightly.
Once the pill bottle reaches its apex and begins to fall back down toward the floor, the situation is reversed - the bottle will accelerate toward the floor at slightly less than $9.8\ \text{m/s}^2$ - and the pills will gently fall back down to the bottom.
Finally, depending on the properties of the pills and bottle, this effect might be swamped by friction or adhesion which would act to keep the pills stationary. Experiments would be required to work out what actually happens on a case-by-case basis.