1099-MISC income is considered self-employment and therefore is subject to self-employment taxes. Even though the amount is less than his standard deduction, self-employment taxes are levied in addition to other tax liability. Even though you son's income less the standard deduction makes his "taxable income" $0, his self-employment taxes are added after that calculation. Self-employment taxes are intended to "make up" for the medicare and social security taxes that an employer would usually withhold and submit. In your son's case, his employer did not pay those taxes and now it is his responsibility at tax time.
