Thanks for your suggestions, finaly found out the reason behind the problem.
The netlist provided was not made case-sensitive. In design which were reported as incomplete nets are all case senstive.
This we can found out by checking in Tools --> schematic viewer of SoC-E.
When i tried it showed 2 nets of same name with case sensitivity like N97 & n97. By making the netlist case sensitive the problem is solved.