The bottom line to your question is that even if your income taxes were not withheld for you, you are still responsible for them and they may have been required on a quarterly basis over the course of 2016 to avoid interest and penalties.  Another issue involves the responsibility for payment of federal and state employment taxes, which are generally split between employer and employee.  A self-employed (1099) worker would be responsible for all employment taxes rather than only half.  
The question of whether you are a W-2 employee or an independent contractor (1099) is a factually specific inquiry into 20 different areas.  Based on the fact that you were W-2 and then it was changed in the third reporting year of your employment begs the question, what factors in that 20 question list changed to give rise to the new characterization?  You may need to bring in a tax advisor who can help you determine if you are an employee or an independent contractor.  As stated earlier, that will not change the fact that income taxes are due from you.