I use workrave in the 'no blocking' mode.  With this mode, it's possible that I continue typing while the break prompt is shown.

The way this problem first started showing was: I have 3 Firefox windows open.  In some cases, when I switched to another window using Alt+` or using the mouse to select another window, keyboard input keeps going to the previously-focused window, and not the new window.

This happens with other software as well which have multiple windows, like gnome-terminal.

Restarting gnome-shell (Alt+F2, r) resolves this issue till it re-appears.  This doesn't happen each time, and what I've mentioned in para 1 above isn't a reproducer, but a guess.

I'm using workrave via the Fedora 22 release.