This behavior is not a bug, but is by design because of Illinois rules. Either you treat them both as residents, or you choose MFS. See the following taken from this website: https://www2.illinois.gov/rev/individuals/filingrequirements/Pages/filingstatus.aspx

If you file a joint federal return and one spouse is a full-year Illinois resident while the other is a part-year resident or a nonresident (e.g., military personnel), you may choose to file “married filing separately.” Do not recompute any items on your federal return. Instead, you must divide each item of income and deduction shown on your joint federal return between your separate Illinois returns following the Allocation Worksheet in the Form IL-1040 Instructions.

If you choose to file a joint Illinois return, you must treat both your spouse and yourself as residents. This election is irrevocable for the tax year. You may be allowed a credit for income tax paid to another state on Schedule CR. For more information, see the Schedule CR Instructions.