Behind the count in baseball is a phrase used to describe a negative situation for either the pitcher or batter in relation to the count. For example, when a batter has more strikes than balls in the count, the batter is behind since he is closer to be struck out. If the batter has more balls than strikes in the count, the pitcher is behind since he is farther from getting the batter out.
Similarly, behind in the count describes who has the disadvantage in the count. If there are more balls than strikes, the pitcher is behind in the count because he is closer to walking the batter than to striking out. If there are more strikes than balls, the batter is behind in the count because he is closer to striking out than to walking.