The cels could be like that because the scene 
required that the cels be pegged on the bottom.  
Now, the reasons for that are plentiful, most of 
which I can only guess at.  Perhaps the scene 
also included cels pegged on top that were going 
to be moving in different ways (slid around with 
respect to each other).  Perhaps someone decided 
it would be easier to paint that way.  

I have heard that US animation has registration 
holes on the bottom by default, the same way 
Japanese animation has them on top.  However, I 
only own one or two pieces of US animation (they 
do have holes on the bottom rather than the top), 
so I can't really say for sure.

Keys
who has a few anime cels with holes on the bottom 
and a few that are even wackier