This is something I often find myself needing to remind trainees about. When performing a step up, make sure to get your whole foot on the box, not just the front part of your foot.
The reason for doing a step up is to build strength and stability in the knees and hips. To build this strength effectively, it is important to apply force evenly throughout the foot. If your heel is not in contact with the box, it will be impossible to apply force through the heel. Instead, you will end up making the exercise too quad dominant. Over time this will under-train the glutes and hamstrings, leading to poor knee health.