Why is the number of pills in the bottle not consistent in 'A Study in Pink'?

There are the same number of pills in each bottle. All the pills in one bottle are poisoned. All the pills in the other bottle are not. The victims only choose the bottle. Once they've chosen the bottle, all the pills in the bottle are the same (either all poisoned or all benign, depending which bottle they picked).

With each victim, a pair of pills is consumed: one from the poisoned bottle and one from the non-poisoned. (Obviously, the cabbie takes a pill from the non-poisoned bottle each time.)

By the time it gets to Sherlock, there is only one pill left in each bottle, because all the others have been consumed. This doesn't change the game at all: he's still choosing the poisoned bottle or the non-poisoned bottle.