The general rule is: your report all your income on your home state return, even the income earned out of state. You file a non-resident state return for the state you worked in and pay tax to that state. Your home state will give you a credit, or partial credit, for what you paid the non-resident state.
If IA is the non resident state:
Nonresidents must file an Iowa income tax return (IA 1040) if their net income from Iowa sources is $1,000 or more.
Reference: https://tax.iowa.gov/im-not-iowa-resident
You didn't really make it clear whether you were an IA or a NE resident. IF you are an IA resident, you would likely have to file an IA tax return based on total income (cutoff income requirements are different), not just the within-IA portion.
For example, I imagine quite a few people living in Council Bluffs, IA work primarily in Omaha.