Military Tuition Assistance Payback

I used TA to sign up for four of my classes. I was only able to complete one class and had to payback the amount for three classes which was $2962.44. On my form 1098-T box #5 (Scholarships or grants) it says that $3949.92 was the amount . How do I claim for the amount of $2962.44 that I paid? Do I contact my school to update my form 1098-T? Any help would be appreciated. Thanks