I believe this can happen anywhere along the 
line; either when the studio releases the cels, 
or by a dealer or owner.  As Lady Brick pointed 
out, it is most likely done to improve 
the "static" image that the cel now presents.  I 
like one like this in my set up; at no point in 
the sequence do both characters have their eyes 
open, but the cel layers are mixed and matched 
now so that they do.

So it's not exactly what you saw on the screen, 
but it makes for a better multiple-layer cel.