This year I started with Covered California and then received employer sponsored insurance

If you had more than one Marketplace plan, enter each 1095-A separately. 

If you had employer-sponsored coverage and a Marketplace plan, enter the information from 1095-A for the months you were enrolled in the plan. The months you had employer coverage will be blank. Follow these steps:

1. Sign into TurboTax. Go to Federal Taxes - Health Insurance
2. TurboTax will ask: Did you have health insurance coverage in 2016? Answer: I had health insurance coverage all year. 
3. Next - Was anyone enrolled in any of these less common (1095-A) plans in 2016? Yes
4. What type of plan were you enrolled in? Obamacare plan (1095-A)

After entering the 1095-a forms it told me I needed to buy the deluxe version. I normally use the free version. It's charging me $60 for deluxe and another $50 for state taxes when I do it online. I think this is a mistake. I think that if I upgrade to deluxe the state taxes should be free.

There is also a Free File program for those who qualify.  

Please check that out below.  

What is the IRS Free File Program delivered by TurboTax?