The OP is not saying the taxpayer was treated as both an employee and independent contractor (which is often dodgy in any case).

By indicating that "they gave him an odd reason why they couldn't and to file it as other income", the employer just appears to be unwilling to report that on the W-2 for whatever reason.  Furthermore, this was given to him as a sign-on bonus (with no reference to this being contingent on services he was to perform outside of his employment capacity with the company).

Under §3402 as well as Treas. Reg. §§31.3402(d)-1 and 31.3403-1, the employer carries the liability for all taxes that are required to be withheld whether or not the proper amount, if any at all, was actually withheld from the employee and would only be relieved of the portion of tax owed (but not the penalties) which is proven to have been paid (e.g. by the employee incorrectly paying over SE-tax).

In the case of worker misclassification, the liability on tax withholdings is dealt with by §3509, which is a different statute.  §3509(d)(1)(B) also prohibits the employer from recovering any tax so determined from the employee and holds the employee accountable for his/her share of FICA under §31.3102–1(d).  That's where F.8919 comes into play.