State tax filing

I filed My NYS tax and NYC-1127 filed automatically but I am a part-year (3 months) nonresidence NYC employee. NYC-1127 was applied full-year for my income and tax(very high) but a standard deduction was applied 1/4 of the portion. It seems quite ridiculous.  How can I fix my NYC-1127? Also I filled out IT-360.1 manually because this form wasn't applied. I uploaded this file on my turbotax document section but the note show "this document will not apply to my filing. Please help me!