It shouldn't be double counted. A 1099 MISC can be entered in either section (as a 1099 MISC or in the self employment income section), as the data from either entry site gets recorded in the same fields on the form and will then display on the coordinating summary screens, therefore there should not be a duplication of data. The two different places to enter the data is purely for to make it easier for the user.
To double check that the income is not reported twice on your return, you can preview your 1040 form before filing by taking the steps below:
https://ttlc.intuit.com/replies/3302322
