Make sure you have this configuration in your tsconfig.json file, the @angular/compiler-cli needs it:
If the ngc (@angular/compiler-cli) command finds any error in your project, it will not generate the code in ‘./dist/ngfactory’
If the configurations are right, and the problem persists, I don’t know what could be wrong, try to clone this repo and see if the same error happens:
git clone https://github.com/evertonrobertoauler/cli-universal-demo
npm run install
npm run start
Let me know if it solves your problem.