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2023 Tax NJ Claiming Underpayment

In 2023, for the first 9 months (Jan to Sep) I was based and worked in Massachusetts for  a pharma company. I have already filed and paid my MA state taxes for the income earned in MA. Starting Oct 2023, I got a new job with NJ based employer and hence lived and earned my wages in NJ from Oct 2023-Dec 2023. Wife also working but she is in NJ full throughout 2023.
 
But my MA employer was still withholding both MA (major part) but some NJ states tax too (~$5K), as my primary home address with MA employer was in NJ as I and my my wife own our home here in NJ. I was only renting in MA. That's why the W-2 from MA based employer also shows NJ address. I tried contacting them to fix it and show MA address after I have left the company in Sep 2023. They won't 

MY CPA filled my MA state taxes for the income earned in MA...straightforward and simple. For NJ, he used my Oct-Dec W-2 (based on my new Job in NJ + my wife's NJ W-2 as she was here throughout 2023) and did a MFJ state filling. This resulted in some refund from NJ, primarily for the state tax that my MA based employer was holding (the $5K)

NJ came back saying I owe the tax on entire income (including everything i earned in MA). So they suggested I file a 1040-X and pay NJ taxes on the whole income and show the MA paid state tax as credit (line 44).
 
This is leading to my entire $5K refund from NJ get wiped off and I instead owe sum to NJ now. NJ has higher tax % by income than MA (5%) for me. 
 
Therefore, I am really concerned and not able to comprehend this issue. Could this community please help how to address this.

At the end of the day, I am happy to pay NJ for the income I earned in NJ, but making me pay state taxes on things I didn't even earn in a high state tax state like NJ is something I struggle with. I already paid due to MA state for income I made in MA. Why NJ is asking to pay NJ taxes on whole deal. I barely lived here for 3 months (Oct-Dec in 2023).

Please guide and help.
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