Without some examples its hard to pin point the problem, but most likely some of the sub-components have the same definition names. You will need to edit each component created from the first one by changing the saved definition names of the subs as well as the parent.
Another possibility is using a common attribute with different formulas in swapping components, but I don't think you are swapping
In regards to the warehouse, there is a hidden attribute which your copied components have inherited.
This can be viewed in Attribute Inspector and then deleted.
When creating copies it is best to use the generic term Parent!anAttribute instead of mycomponentname!anAttribute