I assume the warning refers to this (section 4.2, "Computational Grid" in MOUSE Pipe Flow Reference Manual):
"On the basis of the input data and the specified time step the model automatically generates a complete computational grid, based on the velocity condition (see section 4.5 Stability Criteria (p. 75)). The velocity used in the calculation is a full-flow velocity, obtained from the Manning formulation assuming completely filled conduit. If the velocity condition can not be satisfied for the specified simulation time step, which often happens with short and steep pipes, then the model issues a warning, with proposal for a shorter time step, required for the condition to be satisfied."
You should be able to run your model anyway if you use a small time step, but it might become unstable at high flow rates.