I will fix the tomato / beet problem. By the way, it's only a visual glitch. The window reports you got beet, but you actualy get tomato as you are supposed to. Thanks for reporting it.
Skills can be used outside of battle by going into the "Skills" section in the menu and pressing Q / W, PGDOWN / PGUP to scroll through your party members. Not all skills are usable outside of combat though.