This message means that the elevation drop across the link is less than the minimum allowable drop or (0.001 /3.048 meters)
Elevation1 = Link Offset Upstream + Upstream Node Invert
Elevation2 = Link Offset Downstream + Downstream Node Invert
Internally Elevation1 – Elevation2 should be greater than 0.001 /3.048 meters. If it is not then SWMM 5 or InfoSWMM will use the minimum drop or 0.001 /3.048 meters
It simply is a rule that does not allow flat slopes as the flat slopes mean no normal flow calculations. You should not have to worry about this warning message.
Here is an example of a conduit in which the rule is applied. The rule is applied to link U-104 because it is flat and has no slope.