Excess Roth IRA Contribution (Federal Joint/State Separate)

I'm active duty military and a resident of California while my spouse (non-military) is a resident of Colorado. Because of this I file joint federal, but separate on our state returns. For the state return portion it flags all of my Roth contributions as excess due to my AGI being above $10,000 whereas it is allowed on my joint federal return. Is it correct in stating that I should be penalized for my contributions?