Yeah typically this would only happen to me from abuse of the USO menu and running around the world with Yuffie, Young Cloud (forcefully enabled after acquiring Cait Sith) and Sephiroth in my party. Although it happened a few times with Yuffie, Red, Aeris parties.
What you're describing kuugen, is the method that I knew about but had forgotten how to properly use! haha. I kept making like Triple Cloud parties, running back and forth between screens and in and out of Towns/Worldmap with Triple Cloud Parties, Single Cloud only parties. I ended up just Debug Rooming myself to the part of the game where I was at because nothing else was working.
So...and I know I've seen this talked about in some other places, so I apologize, is there a simple way to go through the game without Cloud in the party? And by that I mean, complete Storyline events without Cloud (or the temporary party leader) being present. Nevermind. Don't answer that, I know it has been asked so many times - I will find the answer after work.