Why does the hydraulic grade line (HGL) show higher flows than the d/D
flow in the pipe?

It is possible that the flows in a pipe are less than the capacity of the pipe (as reflected in a d/D of 0.9 or less), yet the hydraulic grade line (HGL) shows pressurization.

Hydra® calculates the total flows in a pipe (DesignQ and d/D) based on gravity flow — the flow entering the system at that pipe, plus flows from the upstream pipe.  The hydrograph is also base on that same gravity flow.

Hydra calculates the hydraulic grade line (HGL), based on gravity flow plus any downstream flows that may backwater.  To understand better how Hydra calculates backwater flows, please read Chapter 8: Hydraulic Analysis, “Backwater Analysis”.

If your HGL is higher than the flows in the pipe could produce, check the pipes downstream to try to find a bottleneck in the collection system.

This bottleneck could be how the collection system really works — or it could be an unintended data input error.