MT is including my income on tax return and I'm not a resident and my income is from another state?

It sounds like the calculation is working as it should. Your federal adjusted gross income -- even income earned in another state -- transfers over to your Montana return. Your Montana tax is then prorated, based on the ratio of your Montana-source income to Montana adjusted gross income.

According to Montana Taxable Income Calculation in the Instructions for Form 2:

Taxpayers will use their federal taxable income as the base for calculating their Montana taxable income.  Montana's current system uses the federal adjusted gross income as the base for determining Montana taxable income.

See Nonresident Tax in the link above for more information.

As for the filing status issue, you may not be eligible for the Married Filing Separately and Spouse Not Filing status.  According to Filing Status 2c --Married Filing Separately and Spouse Not Filing in the link above:

You can use Filing Status 2c when:

• Both you and your spouse are nonresidents and one spouse has no Montana source income.
• You are a resident and your spouse is a nonresident who has no Montana source income.
• Another taxpayer claims your spouse as a dependent.  When you select this filing status, you must include your spouse's Social Security Number.

Note:  When you use this filing status, you cannot claim your spouse as an exemption on your return.