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Generally speaking, the answer is yes. I don't have experience with minor league teams, but having dealt with professional baseball players, they have approximately 210 duty days in which their income is allocated to the states they play, and they pay taxes in every state they are active from the beginning of spring training. Thus, the employer generally withholds and reports in all of those states.
Additionally, different states have different rules regarding payroll reporting when employees (say other club personnel, like trainers, etc.) are active in that state; however, most states have a minimum number of hours before this kicks in (usually 80 hours, but sometimes as little as 40). That, and the club itself is earning revenue and paying employees in each state it plays; therefore, the club has to file a return in that state and deal with all other employment issues, if applicable, in each state. But, as each state is different, they would have to research the rules in each state they are going to be active in.
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