BUG: Fix return of missing values when applying loc to single level of MultiIndex
- [x] closes #27104
- [x] tests added / passed
- [x] passes `black pandas`
- [x] passes `git diff upstream/master -u -- "*.py" | flake8 --diff`
- [x] whatsnew entry

This confused ``-1`` representing missing values in input with the ``-1`` signaling which components to exclude from output.