You know that part in disk three just before Squall and co. go into Lunatic Pandora and Laguna and Dr. Odine talk about their plan to have Ultimecia possess Rinoa so Ellone can send her in the past to create Time Compression? Odine says he created the Junction Machine Ellone that Ultimecia uses to come back to the past to possess Edea and Rinoa.

Now, I know that for story purposes, they had to achieve Time Compression to fight Ultimecia but... Did it even cross their minds to just destroy the JME so Ultimecia couldn't use it in the future?