It's not hard to do the right thing, either upfront or once you realize you'd done the wrong thing.
The app started with the first four letters of their app name ("Ambi").
they were probably going after any app that started with those four letters, so they would rank higher in searches. Since they used Apple's service, they could probably have had my app taken down, even though there was no way that their claim had any merit.
In that case, I was planning on changing the app's name, anyway (it wasn't a very good name), but I could see this kind of thing being a huge PItA.
I have, however, made the same mistake as you. I work under three different organizations, and can miss which one I have selected (also, Apple is constantly randomly changing the initial one I am logged into). In that case, it was just at the start of development, and I could easily change the bundle ID.