It is possible that your scholarship income, as reported in box 5 on your Form 1098-T, was more than your education expenses, as reported in box 1. When that happens, you have to pay tax on the difference, since scholarship income is taxable if it is not used to pay for education expenses.
That's what I was wondering, however I received no scholarship amounts this year, so the amount in that box is 0. Could it be an issue since my income is coming from the same institution that I'm paying tuition fees to?
*Side note: The tuition slip I have is a T2202
No. One possibility is you originally owed $1,000 instead of getting a refund, it is possible you misunderstood the refund and tax due meter. So, when you entered the education expenses the amount you owed decreased. I can't think of a reason adding education expenses would cause your refund to decrease.