A W-9 is typically requested when an employer plans to issue a 1099-MISC for non-employee compensation. This would be treated as self-employment income on your tax return. However, that is incorrect. As an employee, ALL your compensation must be reported on the W-2, both wages and bonuses. (There are some ways that real estate agents and other kinds of commissioned jobs get around this rule.) by reporting your bonus on a 1099-MISC, the employee is making you responsible for all 15% of the social security and medicaid tax, instead of withholding 7.5% from you and matching it themselves.
As mentioned, you can fix this on your tax return but it will cause the employer to be investigated. (However, the employer won't know that it was YOU who reported it, especially if many employees are in the same position and all take the same reporting steps with their tax returns.)
