You should check if you accidentally ran `npm install` in a parent directory of your project. You can see that by checking if there is a `node_modules` directory. If that’s the case, then NPM will detect that directory as the root of your project and install all modules there.
When there are no other `node_modules` directories in any parent directory of your project up to your home directory or filesystem root, then you should check if your `.npmrc` file has a line saying `location=global`. Delete that line if it is there, because it means any `npm install` command (including the one issued via Yeoman) will install modules in the global spot (probably in your home directory somewhere in a hidden subdirectory).
The NPM config can also be changed by executing `npm config get` (to check) and `npm config set global=false location=project` (to set).