I get retirement pay from the military and have a 1099-R but the program acts like I withdrew money early. Also not sure if qualified or non qualified plan

First, double check that you chose the correct code for Box 7 on the 1099-R entry screen.  For normal military retirement pay, Box 7 should have Code 7 - Normal Distribution.  (If you entered an incorrect code, such as Code 1, TurboTax will think it was an early distribution.)

Military retirement is a non-qualified plan.

To get back to your 1099-R:

• Once in your return, type "1099-R" in the search box on the blue dashboard
• Click "Jump to 1099-R" link
• Click Edit next to your military retirement 1099-R. 

This answer is incorrect. It should be a qualified plan. You will get an error if you say nonqualified.