When HEAT zip was contains files: 
HEAT.meta 
vendor-license-model.xml 
vf-license-model.xml 
and they were added to manifest by user (by mistake) - no heat validation was run and VCF creation was failed only on packaging ( csar creation). 
It was failed because these files generated by SDC but they already was part of HEAT. 

To fix it - heat validation was added: 
if one of generated by SDC files is part of HEAT zip and theys associated in manifest file -> new error message will appear and VCF will not be created. 
Error message: 
     Artifact with file name %s is generated by SDC. 
     Please remove this artifact from manifest and zip files