Actually, Eclipse itself can have multiple consoles open at the same time... if you want, you can create multiple console views and pin a different console to each view (if you don't pin the console, one console will be shown on top of the other and you'll have to do the switching from one to the other manually).
As it is now, the debug console is not the same as the interactive console (it's a simpler version because of issues with the eclipse integration, although there are plans to be able to attach an interactive console to a debug session).
So, what you described is what should really happen (not really a bug).