The project manager should have analyzed the boundaries of the negotiations for agreement to prevent this situation. This involves understanding the company's policies on core working hours and negotiating a schedule that aligns with the team member's needs while adhering to organizational norms. By doing so, the project manager could have ensured that the alternative working schedule was acceptable within the company's framework and avoided scrutiny from other teams. It's important to balance the flexibility required by the team with the expectations and standards of the broader organization.
References: While I can't provide direct links to the specific documents, the principles outlined here are in alignment with the PMI's standards and guidelines on project management and negotiation within the context of organizational policies and stakeholder management.