Special:GlobalPreferences does not deal well with "conditional preferences" (using hide-if). When a preference is hidden because the conditions to show it are not met, the checkbox to set it as global is still visible.
Currently this affects two preferences (testing on https://en.wikipedia.beta.wmflabs.org/wiki/Special:GlobalPreferences):
User profile → Newcomer homepage → Default to newcomer homepage from username link in personal tools (only shown if Display newcomer homepage is checked)
Appearance → Vector skin preferences → Use Legacy Vector (only shown if Skin → Vector is selected)
QA Results - Beta
QA Results - Prod