"did you pay federal income tax in 2016?" Is this asking if when i filed my taxes if i owed? or is it asking if i paid throughout the year, because doesn't everyone pay?

It is asking if you owed and paid federal tax when you filed.  Sorry if that wasn't clear.  I will take a look at it to possibly send in for clarification.

Strongly suggest clarification

Yes I agree. This needs clarification. Almost everyone pays federal income tax but apparently what the question is really asking is: When you filed your taxes did you have to pay additional income tax?