Any files from the source directories ./node_modules/.bin directory won't be copied over.
This can cause issues if you're copying modules with binaries since you'll have to manually copy over the bin folder yourself.
copy .bin folder still can't solve the issue. Since .bin files are not real files, it's more like a link to the real file. If you copy .bin folder, these "links" will become real files which may cause module not exist issue. See this answer.
Any files from the source directories
./node_modules/.bin
directory won't be copied over. This can cause issues if you're copying modules with binaries since you'll have to manually copy over the bin folder yourself.