What version of Turborepo are you using?

1.7.2

What package manager are you using / does the bug impact?

pnpm

What operating system are you using?

Mac

Describe the Bug

Running pnpm prune after pnpm i at the root level will produce a broken lockfile.
This behavior is leading to this error  ERR_PNPM_LOCKFILE_MISSING_DEPENDENCY 

Expected Behavior

lockfile should be correct

To Reproduce

To reproduce the bug

1. git clone git@github.com:Marwennnne/turbo-prune-missing-dep.git
2. cd turbo-prune-missing-dep
3. pnpm i 
4. turbo prune --scope=web --docker
5. mv out/pnpm-lock.yaml out/json/pnpm-lock.yaml
6. cd out/json && pnpm install --frozen-lockfile --strict-peer-dependencies

But when I delete the node_modules at the root level and I rerun the commands 4,5 and 6 lockfile is produced correctly meaning I should not install dependencies at the root level

Reproduction Repo

git@github.com:Marwennnne/turbo-prune-missing-dep.git