Hello,
This can only be explained if the depth at the entrance is 0 everywhere, which is not the case if you are right, OR if the prescribed velocities are 0 for some reason (depending on how the discharge is imposed or which kind of velocity profile you use). The subroutine that complains is debimp_3d.f (it replaces an older debimp3d that has been kept in the library for compatibility, so old subroutines bord3d may still contain a call to debimp3d). The minimum depth is -1000., so it should not interfere. Please note that you have also a keyword : THRESHOLD FOR VISCOSITY CORRECTION ON TIDAL FLATS which is by default 0.2, and that you should probably change in your case which is probably a physical model (it is not the reason of your problem, but may change the results).
Regards,
Jean-Michel Hervouet