The fact that the school was paid directly, rather that you being reimbursed, does not change the answer above. That's fairly common. However, your employer is allowed to pay third parties (a college in this case) for job training, and that is a business expense to them. Apparently, your employer is calling it that, by selecting the courses and not including any of the money paid, on your W-2. The fact that you also end up with a degree (the courses were not TOTALLY for the benefit of the employer), probably does not change the job/business classification of the courses. Whether it does or not is between them and the IRS and not your concern (most likely).
Therefore, yes, it was correct for you to not include the 1098-T in your tax filings. You cannot claim a tuition credit, since you didn't pay any tuition. If there was an amount in box 5 scholarships (there shouldn't have been), you do not need to report that either, since it went for job related education.
