All commercial roofs will have some sort of waterproof membrane layer as the primary water barrier.
Damage to this barrier can come in the form of heavy foot traffic, natural occurrences such as hail, wind, falling branches that can puncture or tear the membrane as well as damage due to mechanical issues such as HVAC and other non-roof related maintenance issues.
One common issue is when standing water collects on the roof. Those puddles also collect dirt and debris. As the water evaporates, the dirt and debris stay and create a dark spot on the roof. The sun raises the temperature in these areas, especially on white roof membranes like TPO and PVC. The rising temperature breaks down the membrane causing commercial roof leaks and failures (learn more here).
Most often, damages can be successfully repaired with patchwork done by a trained commercial roof repair technician.
In other instances, a larger membrane section may need to be repaired. The insulation may need to be replaced. There also could be structural work needed depending on how long the repair goes unattended.