We have observed problem in the number of SetPass Calls reported between the Unity Profiler and the Frame Debugger, especially when analyzing complex scenes with heavy rendering. Upon investigation, we believe this difference is expected due to the working nature of the Frame Debugger.
Below are the key factors contributing to this behavior:
Frame Debugger replays, not records: The Frame Debugger does not capture the exact GPU execution. Instead, it replays rendering operations step by step using the CPU, which includes temporary render targets, shadow passes, and UI layers. This replay process adds additional SetPass Calls that would not normally appear in runtime execution.
Editor UI overhead: Opening the Frame Debugger itself introduces additional editor UI draw calls. Unity has to redraw internal windows using IMGUI or UI Toolkit, which results in increased SetPass Calls unrelated to the actual scene.
Live rendering interference: When the Frame Debugger is opened during live scene playback, it adds overhead while trying to snapshot a moving frame. This further complex the representation of actual draw call behavior at runtime.
Scene complexity amplifies the effect: In scenes with multiple layers, post processing effects, several rendering passes, the replay becomes heavier and introduces more variance this adds to profiler when we navigate the frame debugger during runtime.
Recommended workflow: For a more accurate representation of draw calls and SetPass Calls, we suggest using the Profiler to record the frame first, then pausing the editor and opening the Frame Debugger for analysis. This avoids the impact of real-time UI redraw and editor overhead.

Sometimes it can also be helpful to use an external tool that captures and stores a single frame, for instance RenderDoc or Xcode.