This is an annoyance I have overcome by moving the Apps into alignment, and gradually the bottom ones reappear. But agree the “App Map” you are talking about (this also needs a name in the Fibery vernacular) should not have this happen by default, or at least there should be info on how to fix it easier. This took me an age to figure out, and asked support to help, who didn’t actually know how to fix it, either!
This is a great feature though, and I’d like to plug again for a feature that would do the same automatically, but at the Type level. Would help solve some of the missing “auto-generating” whiteboard functionality, too: