This is a small bug, that just happened once. I unchecked all my variables so they would disappear. But one of them, “Code”, was still there, and the place which was meant to be the orange variable box was gone and was a completely white square. It fixed itself when I tried checking and unchecking the variable.

This is a problem with the screen not refreshing entirely. It plagues practically all computer programs, and I have seen the exact same thing happen myself. To prevent lag, computers only refresh the sections of the screen that they have to (when a sprite moves, variable appears/disappears, background change) and sometimes the calculations are off a bit. This happened a LOT with 1.4 whenever a sprite moved quickly.