Interesting! If it happened on the PSX version too, Square's beta testers have failed to uncover it not once, but twice.
"Fool me once, shame on you. Fool me twice...you can't get fooled again!"
~George W. Bush (edited per chrono eric's superior memory)
EDIT: Also, it happened to me on the SNES version. I *distinctly* remember this, and a bite mark on my SNES controller serves as physical evidence. Thus, the End of Time save bug is a running bug throughout all versions of Chrono Trigger! Players beware!