Can an employee file a Schedule C for work with the same employer? They gave him both a W-2 and a 1099-MISC with box 7 Nonemployee compensation.

Sounds like the employer is trying to save some payroll taxes.  What were the 1099 pmts for?

Ddvols gives an example of a scenario that I've seen several times over the years (W-2 secretary during the day; 1099 occasional cleaning person at night). That's perfectly legit.

Form 8919 coupled with Form SS-8 would be the recourse if the employer has been playing fast and loose with the employer/employee relationship. Three considerations: (1) As someone pointed out, it had better be an ex-employer because filing those forms essentially puts the employer on report with the IRS. (2) Make sure the client knows that if he wins, once all the dust settles he will save only about 7.65% of the amount (or "profit") on the 1099, so he should consider carefully the pro's and con's of lighting the SS-8/Form 8919 fuse. (3) Having lit the fuse, there is no guarantee that the IRS will ultimately side with the employee over the employer, although admittedly the IRS goes into the decision leaning towards an employer/employee outcome versus an independent contractor result. I've handled only a handful of these cases, but in every case, the IRS ruled in favor of the employee.

Finally, I didn't follow Shorebird's "take off the expenses subject to 2%" comment. I might be missing something here.

This would never fly in my State: "(W-2 secretary during the day; 1099 occasional cleaning person at night). That's perfectly legit."

First, unless the person has a cleaning business and cleans at other locations, too, and is using their own supplies and tools, then all you have is an employee with multiple tasks or duties. Next, our Worker Comp service is run by the State, and they have issued guidance on this specific subject, that you have no way to show "when" the person hurt their back while on the job, no matter what worker classification someone tries to apply to justify a 1099-Misc along with a W2.

It's not unusual to issue a 1099-Misc for box 1 rent to a mechanic with their own tools or a trucker for the use of the truck or renting their fifth-wheel trailer for on the job needs. You also see 1099-Misc for lawsuit settlements. It's pretty easy for the person to look at their W2 compared to what they know their wages should be, to see if this 1099-Misc is part of it, or in addition to what they expect their gross to be.