There are several reasons for bad breath. The main culprit is bacteria that is not removed from the mouth. The tongue holds bacteria, and if not properly cleaned when the teeth are brushed, then the bacteria is still present, which can cause bad breath.
In addition:
A person with periodontal disease will have bad breath due to bacteria.
Decayed teeth can also cause bad breath.
Acid reflux can cause bad breath due to the misplaced acid in the esophagus.