Anyone else notice this, or am I totally crazy?

In the final showdown with Zeromus, Cecil and his party are all laying there pretty much dead. Then we cut away to the Elder and his buddies in Mysidia all wishing for Cecil and crew, and they are revived and proceed to fight the big ugly Zeromus.

Now, I want to know if anyone else saw this. When the screen fades out from the Elder in Mysidia and back into the final room with Zeromus, Cecil and everyone, the screen seems to fade in really dim at first, and you can see people move into place really quick, then the screen lights up the rest of the way once everyone is in position, laying on the floor. It's like watching a play and seeing the actors get into position under really dim lighting.

I think it may only be on the SNES version. Anyone else notice it?

No, but I'm not surprised. The way the battle system was programmed, it may have been impossible (or at least inconvenient) to open a battle scene with the party already in position.

Yes, mostly likely the battle system required the developers to spawn a new battle, move everyone in place and then set a KO status on everyone.