I've never encountered this bug myself, nor heard about it happening in the SNES/PSX versions. After reading the posts on GameFAQs, and now here, I decided to investigate.
The problem occurs if the characters are moving when a save point is activated. It is possible to be out of bounds of the save point during the time the menu is activated and the screen transition is complete. Upon saving, instead of saving the exact coordinates, the value gets rounded. When the save game is loaded later on, the character could be stuck in the wall.
To avoid this situation completely, stop moving before activating the save point.
If you do get stuck in the End of Time, enter the menu, and the instant you press the button to exit, hold the d-pad and dash button towards the open area.
Youtube video:
http://www.youtube.com/watch?v=EmeQlSdDeMQThis video was done on the SNES version.
Other confirmed SNES locations:
Location 17C - Terra Cave
Location 194 - Ocean Palace entrance
Location 19A - Ocean Palace (the second save point)
Location 1C2 - Black Omen (save point before Queen Zeal battle)
Location 1DA - Lavos tunnel
Location 1EF - Death Peak cliffs
Unlike the End of Time, it doesn't appear possible to escape if you get stuck in the wall in these areas.