Limitations

1. npm-shrinkwrap.json and package-lock.json are ignored. Unlike pnpm, npm can install the same name@version multiple times and with different sets of dependencies. npm's lockfile is designed to reflect the flat node_modules layout, however, as pnpm cannot create a similar layout, it cannot respect npm's lockfile format. See pnpm import if you wish to convert a lockfile to pnpm's format, though.
2. pnpm can't publish npm packages with bundledDependencies. Currently, there are no plans to add support for bundledDependencies either, as they do not work very consistently in publishing, even on npm. Instead, we recommend you use an actual package bundler, like webpack, rollup, or ESBuild.
3. Binstubs (files in node_modules/.bin) are always shell files, not symlinks to JS files. The shell files are created to help pluggable CLI apps in finding their plugins in the unusual node_modules structure. This is very rarely an issue and if you expect the file to be a JS file, reference the original file directly instead, as described in #736.
4. Node's --preserve-symlinks flag does not work when executed in a project that uses pnpm.

Got an idea for workarounds for these issues? Share them.