1) Did your client telecommute from NY during those 2 weeks?  If not, there should be no NY-source compensation and a W-2C should be issued.

2) Sounds like it's a problem with how the return was coded for NJ and NY.  You may like to check all your input again and refer to the following articles for reference:

https://proconnect.intuit.com/community/help-articles/help/how-to-create-a-multi-state-return/00/471...

https://proconnect.intuit.com/community/help-articles/help/input-multi-state-amounts-in-proconnect-t...

https://proconnect.intuit.com/community/help-articles/help/entering-w-2-wages-and-withholdings-on-mu...

https://proconnect.intuit.com/community/help-articles/help/how-to-enter-part-year-or-nonresident-sta...