Although my employer only allows tuition reimbursement for undergrad classes, they knowlingly made a special acception for me in order to take graduate level courses. Something that other employees asked about and were denied. As a condition of the tuition reimbursement agreement, I was asked to sign a document stating I would remain an employee for 1 year after collecting tuition reimbursement. I am planning on leaving the company and it has been under a year since signing this document. The supporting documentation that I provided to them when I registered for classes clearly states that this is for graduate level courses and was signed off by 3 Managers. Is the fact that they made a special acception against company policy make this agreement void since it specifically spells out in the agreement that only undergraduate level courses are covered under this agreement?

You will not be reimbursed for these courses regardless if they were undergraduate or post graduate UNLESS you work for the company for the one year provision. If you leave their employment they can and will probably sue you for the money they paid out to you and you did not keep your end of the agreement. It has nothing to do with 3 managers signing anything. It has to do with you not staying employed. (How hard is this for you to have figured out on your own if you went to college I wonder.)