you can just ignore these errors, they are kind of "expected". Couple of files are being removed during the build process as we don't require them within our application (to save same space). But as they are still referenced within some libraries, the ngen does throw out some "file does not exist" errors.
ok Thought so, Thank You.
I ran the ngen.cmd file as directed from the downloads page and I have attached a log file of errors from the ngen log from (C:\Windows\Microsoft.NET\Framework\v4.0.30319). I have replicated it on a VM as well and get the same errors. It looks like there are some files missing.
Hope this helps. Not sure if it is ignorable errors or not but just thought I would bring it to your attention.