My employer mistakenly withheld NY taxes, filing as a nonresident in Turbotax is not giving me the full refund

I live and work in FL, but for a month or two, my employer withheld NY taxes mistakenly. They told me that I needed to file NY state taxes as a nonresident and declare $0 earnings in NY and I would be refunded the withheld amount.

I tried doing this in Turbotax and of the $2000+ that I was withheld, I'm only being refunded ~$1300. Is this because that refund is "taxed" or something?

I also would like to know what's the correct process through Turbotax to rectify those erroneous withholdings since I might not be doing it right.

Thanks!