It is possible there was something inadvertently not included during the Michigan Nonresident interview to indicate the 1099 should be taxed in Michigan.
When doing nonresident and resident returns, always end with the state where you lived on December 31. The nonresident state should be entered before the resident state.
For more information, see: How do I file a nonresident state return?
2020 Michigan Nonresident and Part-Year Resident Schedule Instructions.
