This is easy to reproduce in the Keyboard Configurator by holding down the ctrl key (for instance) while remapping it to something else using the mouse. On releasing the key, it remains stuck, regardless of other key presses. (This state is resolved by unplugging the keyboard and plugging it back in, for an external keyboard.)

This may be easier to accidentally do with some of the new features being added to the Configurator.

QMK has clear_keyboard/clear_keyboard_but_mod/clear_keyboard_but_mods_and_keys functions, used for instance on layer switching. Not sure what is appropriate here. Also need to verify that it doesn't cause a noticeable issue with many keymap sets in a row (layout import/reset).