If you comprehend something, you know what its meaning is or why it is the way it is. Comprehend is only used in fairly formal or literary language, and usually with a negative to say that someone cannot comprehend something.
1. Her face was blank and numb as though she could no longer comprehend the reality around her.
2. He could not comprehend how Grant had ever been selected for this mission.
It is much more usual to say that someone understands a situation or a problem.
3. “And because I can go no further, you must go alone. Do you understand?’”
4. Morris felt he understood more deeply, now, what McLuhan was getting at.