Commissioning issues and deficiencies can be identified through a combination of visual inspections, performance testing, and data analysis. During the commissioning process, professionals should review design documents, inspect installations, and perform functional testing to identify discrepancies between the design intent and the installed system. They should also analyze system performance data, such as temperature, pressure, and flow rates, to detect anomalies and inefficiencies. Furthermore, interviews with building occupants and facility managers can provide valuable insights into system performance and identify areas for improvement.