The GPA calculated on your transcript is a weighted GPA. This means that courses marked as Honors, Dual Enrollment, or Advanced Placement (AP) receive extra "weight." Though this can result in a GPA that is higher than 4.0, most colleges accept and even prefer weighted GPAs.
The weighted GPA is calculated this way: Advanced Placement (AP) and Dual Enrollment (DE) courses receive an extra 2 grade points. Honors courses receive an extra 1 grade point. So when the grade points are calculated for a single course, you would have to add 2 to that course if it's marked as AP, for example. That would result in a higher, weighted GPA.
If you wish to change the weighting to suit your needs better, you are able to do so. Please reference our article, How Do I Change Course Type Weights?