Yes, this happens on my Nexus 7 once in a while. It's happened 3 times with the SwiftKey application. That app stays on the device, and I can see it in the Settings/Applications screen and drag it back to the desktop. When this happens, it becomes "unregistered" as the default keyboard, and the Google keyboard asserts that status.
And just now, some other app icon disappeared right before my eyes. I don't know which one it was, because it was an app that I almost never use... I don't have a spatial memory of what that location on the home screen did for me.
I'm still happy with the Nexus 7, and glad that I took a chance on it, rather than buying an iPad. This bug is annoying, but not a "device flusher".