I am working for a company out of town. There have been a few things that haven't gone as planned. At the moment some people are getting their pre diem and others are not. Is there a NY State law that answers this question? Can a company pay some people pre diem and not others?

Per diem ? Are you an employee or a contractor? Yes, company can do as it chooses depending on contract. Clarify your situation. "There have been a few things that haven't gone as planned".

There is no law requiring a per diem. This is a matter of union or employment contract.