I am a CA resident in the military stationed in NE. I was legally a resident of CA for the whole year but am being asked to fill out the Worksheet for Part-year residents

You are correct.  Since you are active duty you are a resident of California because that is your state of residency.  You will want to double-check a few TurboTax entries.  First, in the Personal Info tab, you should have answered no to the questions if you lived or worked in another state.  Even though you were stationed in Nebraska, you are not considered to have lived or worked in Nebraska.  Checking these boxes separately might eliminate the message.

Also, though, make sure that your W-2 is marked as active duty military.  You can do this by checking the following:  

1. Sign in to TurboTax Online, click take me to my return, then pick up where I left off.
2. Click on Wages and Income, then Edit on your W-2
3. Scroll through the screens until Do any of these uncommon situations apply?  Make sure the Active Military Box is checked. 

Finally, one other place you want to check is in the California state return.  California passed a law last year that exempts military income by California residents when they are not stationed in California.  You will want to answer any question about how much income was earned in another state with the amount of active-duty pay you earned stationed outside of California.