Your employer is correct, there is no such thing as negative income form exercising stock options with a strke price greater than the market price. As for how to report your loss, have you sold the stock you received when you exercised the options? If so, you should have received a Form 1099-B for that sale. If you have not sold the stock, you only have an unrealized loss, which you cannot claim/deduct on your tax return.
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