Greetings
I was confused by this same thing. I started playing EU3 only recently, and it is my first grand strategy game. I encountered this oddity very early, but the complexity of the game was so puzzling at first, that I couldn't really tell what actually was a bug and what was just weird game design. After a few days however, thanks in big part to the good wiki, I managed to get a handle on it, and I got convinced that this strange instant loss thing must indeed be a bug. So when it once happened right after a save, I tried if I could reproduce it. And I could. After that I searched for it online to see if others were experiencing it too and if there was a solution to it. And when I found this thread, I was surprised that even on the official forums most of the regulars aren't familiar with it. (Perhaps it isn't encountered as frequently if you play the more rational countries...) So I'm posting it here to shed some light on it.
I didn't really like most aspects of the game design either, but perhaps I could live with them. This bug however was a real game breaker for me. Now, I know that this game isn't a FOSS project but a rather old commercial title, so I don't presume the developers will fix it. I'm simply posting it for the sake of clarity.
Still, I liked the core idea of the game. Perhaps I should try their newest generation. I got CK2 last week for a bargain price in a Humble Bundle, I hope I will be much more happy with it. The reviews are very promising, and if I won't, well, it cost me practically nothing. Definitely will try EU4 too, if I catch it on sale.
As for the bug, here's the explanation: The rebels in Mogadishu are loosing, after the battle they retreat to Lamu and instantly destroy my army there (it has good morale). In the first save game, where they're still in battle, the bug doesn't occur every time, usually the rebels get defeated because of their lower morale when they get to Lamu. The second save game however, where they are already retreating, is one of the buggy outcomes, and they instantly destroyed the army in Lamu every time i reloaded it.
The version is EU3 Complete on Steam.