There are a few reasons for this. First, depending on the speed of your metabolism, it may take up to 20 minutes for the alcohol to be absorbed into your bloodstream. Until it is fully absorbed, the breathalyzer cannot give you an accurate estimate of your BAC.
Second, after you take a drink of alcohol, the air in your mouth and esophagus is laden with the substance. If you were to breathe into a breathalyzer right after drinking a shot, for example, your BAC estimate would be very high—and also very inaccurate. Waiting 20 minutes allows the air in your mouth and esophagus to return to a normal level.
Lastly, it is important to make sure the mouth is clear of contaminants (including smoke, food, and liquids) as objects other than air getting into the breathalyzer can damage the sensor and cause it to malfunction.