I've noticed that, especially with Utena cels,
correction layers seem to be pretty common.  I
have probably half a dozen cels that have this
sort of a correction layer on them... it's 
usually there if something wasn't shaded that
was supposed to be shaded (or visa versa), or
sometimes even to completely correct colors and
details (like in a Sword-pull-bank-cel I have
of Utena and Anthy - the correction layer has
new colors and details, I guess because the
painter goofed and didn't want to repaint the
cel).  

My best example of this is probably my Jury cel
(episode 12).  This is an A1END cel, so I don't
have others in the sequence to compare it to,
but the scene takes place in the evening - the
original layer was painted with Juri's usual
colors (bright colors), and the correction layer
makes the colors slightly more muted to reflect
the nighttime atmosphere...

Lady Z