Yes, it happens... and it makes more sense for it 
to happen at the studio while filming, as opposed 
to post-production, when there's no real reason 
for them to take the time and effort to chop up a 
cel and tape it back together after filming.

For mine, it's a two-layer setup. The A layer has 
its top inch (with the holes) sheared off and 
taped to the bottom. The B layer also had that 
treatment, but the strip probably fell off at 
some point in time, and all I have are the 
sketches to get its layer number by. For my 
setup, I don't mind so much that the cels have 
been altered, as much as I mind that the cels are 
stuck together. ^_^