Issues with 'pnpm install' using t3-turbo-and-clerk

I'm not sure if many people are using the 't3-turbo-and-clerk' template, but I'm having an issue where pnpm has very inconsistent and erroneous package installs. When I first cloned the repo, it was working correctly, but now when I run pnpm install it will install all packages to the root level node_modules. If I use a different version of pnpm it might install node_modules in the apps/packages, but it's an incorrect and incomplete installation. I've been stuck trying all kinds of things for a day now. I delete the pnpm-lock file and do a 'clean' before installing each time, but with no luck. Even pnpm clean only cleans the root level node_modules... I haven't touched pnpm-workspace.yaml or any config files, so I'm leaning on it being a PNPM issue, but I have no clue right now. Anyone have any thoughts? screenshot is an example of the incorrect installion I was talking about... in my apps/nextjs folder, this is what it installed for node_modules.