Opus pointed out that there are two different types of FSAs which are treated differently. Please tell us if you have a health care FSA (for paying medical bills) or a dependent care FSA (for paying dependent care bills). Until you tell us which one you had, we can't be sure of your issue.
Based on what you have said so far, it sounds to me that you have a dependent care FSA. As Opus asked, do you have a dollar amount in box 10 on your W-2? (My guess is yes). When there is an amount here, you have to complete form 2441 to show that this amount (or part thereof) was covered by documented spending on dependent care. Did you go to the Child and Dependent Care interview, and what questions and answers did you make there?
If you had an entry in box 10 on your W-2 and did not correctly complete the Child and Dependent Care section, this would cause the amount in box 10 on the W-2 to be added to your income, as Opus said at the end of this post.
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