Mani
Initially, you can go through the start time and end time of simulation defined in both the MIKE SHE model and in the MIKE 11 model. The reason for the problem may be that these are inconsistent. This is normally not a problem as MIKE SHE will decide which time interval is executed in a MIKESHE-MIKE11 simulation, but it may be an issue in your version of MIKE SHE.
If you do not manage to find a solution, I would recommend to ask MIKE support at mikebydhi@dhigroup.com
Regards
Torben