Correct. WiX compiler MakeSfxCA.exe doesn't know that the NuGet package needs to be included in the CA package as NuGet is a VS package manager and it has no integration with WiX.
Thus all non-GAC assemblies the CA depends on must be added to the Wix# project so they are available at runtime. See DTF_ExternalAssembly sample for details.
If you are using ManagedProject then you need to add the assembly to the project:
Thus all non-GAC assemblies the CA depends on must be added to the Wix# project so they are available at runtime. See DTF_ExternalAssembly sample for details.
If you are using ManagedProject then you need to add the assembly to the project:
project.DefaultRefAssemblies.Add(typeof(LibA.ClassB).Assembly.Location);