What to do with 1099-MISC that is for regular full-time work but not for self-employment?

I was issued a 1099-MISC in addition to W-2 from the same employer. I stopped working for that employer, and according to payroll, 1099-MISC was meant to cover my pay in the "final paycheck waiting period" from which tax was not withheld, which was because my final check was not processed in time based on my state's regulations. I would think this is for income for my regular work of my full-time employment just like what is reported on W-2.

After I entered it on "Form 1099-MISC" (the amount is in Box 3 of Other income) under "Other Common Income", an item "Self-employment income and expenses" appeared for me to review in which I am asked to fill in information that looks odd to me, as if I were self-employed. Since I was not really self-employed and the income reported on 1099-MISC was for work performed during my full-time employment as mentioned, what should I do to proceed?

BTW, I am a resident alien and my nonimmigrant status does not allow real self-employment. Therefore, I would like to handle this cautiously to avoid troubles later on.