Yes, it happens. I had a similar situation. Sometimes, in order to return the overpaid taxes, you need to contact the tax company after a while. Usually after receiving the W2 form. You can come with your W2 form and prove that you have paid more taxes than you owe, then they will probably be reimbursed to you, but most likely they will be deducted from the amount of the following tax deductions. You will be able to estimate the amount of tax payments on the W2 form online at https://www.thepaystubs.com/w2-form-generator to find out how much money you can return. But this will not work if you live in a state where tax-exempt organizations must pay taxes on their own goods.