Trying to get military spouse income tax returned

Each state has its own rules when it comes to state taxes and military tax treatment.   Since your home of record is FL, she can use FL or CO as her resident state.   If she uses FL as her resident state, she needs to file a nonresident return (that link has instructions) in CO.   If she uses CO as her resident state, she will file a resident return in CO.   

I am assuming you are military and she is non-military and you are filing a joint return for federal tax purposes.   

Military Spouses and State Taxes     See below for information specific to military spouses in CO.  

For tax years beginning on or after January 1, 2009, a military spouse may be able to exclude their wages and tips from Colorado income tax, in certain circumstances. The spouse must meet all of the following criteria:

• The service person and their spouse are married.
• The spouse moved to Colorado from another state and the spouse works in Colorado.
• The spouse's sole purpose for being in Colorado is to accompany the service person while they are stationed in Colorado on military orders.

The spouse would need to file a DR 0104PN form to apportion their Colorado-sourced income each year.  Additionally, the spouse should submit a DR 1059 to their Colorado Employer when they are hired. Then the spouse should submit the signed DR 1059 to the Department each year when filing their tax returns.  Note: This form is needed for the employer because the employer would be required to withhold income taxes if the spouse works in Colorado.  If the employer does not withhold any CO state taxes from the spouse's paycheck, then the employer would need the DR 1059 on file.  Additionally, the spouse must provide the Department with a copy of the service member's military orders and a copy of their military ID.

Get those forms in ASAP to stop her employer from withholding.  Try completing her state return as a nonresident and resident to see which produces the greater refund for this year.  TurboTax will follow the rules for each state, so there is nothing you can click on in the program to cause an automatic return of her withholdings.   But you may try contacting the state to see if there is anything you can do to recoup the withholdings you don't get back on this return.