MO does charge a penalty for unpaid taxes. If MO believes you owed more money earlier in the year, they could be charging you a penalty even though you are getting a refund. PY residents can elect to file as residents or nonresidents. The state does look at your income for the full year and calculate a tax liability. Then it prorates the amount based on MO income divided by total income.
Since you moved there late in the year, a penalty does not make sense for you. Check your dates of residency and entries. I wonder if you had MO income all year and just moved there later to create the penalty.
You may need to contact support to have another set of eyes look or maybe you could post more information about what is causing this - sale of property vs income. Lump sum vs spread out. Is the penalty being charged on the full income instead of MO income?
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