It appears you will need to pay NE taxes. Here is an extract from NE Code 316 Chap 21 which is guiding your employer.
"001.02 Every employer paying any wages to a resident or nonresident individual must deduct and withhold for the Nebraska income tax if:
001.02A The employer is maintaining an office or transacting business in Nebraska;
001.02B The wages are taxable under the Nebraska Revenue Act; and
001.02C The wages are subject to withholding under the Internal Revenue Code (I.R.C.), as amended.
And here and extract from NE Code 316 Chap 22 for paying NE income taxes.
"002.02 Nonresident individuals. The Nebraska individual income tax is imposed for each taxable year on the income of every nonresident individual which is derived from sources within Nebraska."
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