Disputing W2 wages

Basically a friend worked for a company that was bought out. She worked for the company for 2-3 years, forfeited bonuses along the way in exchange for equity. The company was bought out for a significant amount in 2015 and she received a W2 for about $450k. Regular wages would have been around $100k for the year, the rest is related to the buyout. She was under the impression that some portion should have been capital gains income.

My question is, can she file her return with the W2 as is (as to avoid penalties for late filing), but later appeal to the IRS that the income should have been reported differently? If that is possible, what kind of documentation would be needed? Thanks in advance.