Multiple assemblies with equivalent identity have been imported: '<in-memory assembly>' and '<in-memory assembly>'
All, After chasing it for couple of days and multiple experiments. I have narrowed down. The issue is I was trying to push the asp.net vnext application only with dnx451 framework. After including the dnxcore50 I was able to push the application into Docker Container inside Windows Server 2016.
"frameworks": { "dnx451": { }, "dnxcore50": { } },