I don't think there's anything "fishy" here. It appears you employer does not have a formal tuition reimbursement plan, meeting IRS regulations*. He has (generously, in my opinion) provided you informal help. He is required to treat that help (benefit) as taxable income.
Since your past year tuition was effectively paid with your after tax money, you should have claimed the tuition credit in each of those years. If you did not do so, you can file amended returns for those years to claim the credit. You can still file amended returns for 2017-19. The more generous American Opportunity Credit (AOC) requires you to be at least half time and a degree seeking undergrad. The other credit and deduction are not as restrictive. There are AGI limits, so if your filing status is Single, $80K MAGI would disqualify you. There are no other deductions available, unless the education was work related. Then, you might be allowed an itemized deduction (for 2017 only, rules changed in 2018), subject to the 2% of AGI rule.
*The tax free limit is $5250, per year. A qualified tuition reimbursement plan would only be allowed to pay that much, tax free, in 2020, even though the payment was for multiple years.
