Cool suggestion: Eatable MOUSE-pointers. Have you used the Advanced Search today? Need help, question? FAQ -Wiki -Forum help I still like small signatures...
I suggest improvement to blueprint GUI which would stop this bug/not bug discussion and also would allow us to make better blueprints!
Basicly, when we select some area for a blueprint (for example part of existing factory) all the entities inside this area are taken into blueprint, and in GUI window shown afterwards where you choose icons etc, there is a list of this items (Totals).
Here's the suggestion:
Make this items clickable (in Total, not on preview ..) - and clicking on item would remove it from blueprint! May it be - all items of same type, to make it easier to implement.
Then you could show the modules from inside the buildings in items list! So if someone wants to make blueprint without modules then he would just remove them before clicking Create Blueprint button.
One more thing missing here is that bots can't put modules into buildings right now... so would need to implement "ghost modules" or something like this But even before it's made (if...) my suggestion seems still useful!