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Did I do something wrong?
Have you linked both sites to each other? For what you say it seems that both sites share the same content. If that's the case it doesn't matter that the domain names are different. Basically you have triggered a duplicate content filter.
Is that the case? Do both sites have exactely the same content?
I actually have the .net, .org, and .com of my business name, as well as the old URL (which I don't really care about, since it's not my branded name).
How do I fix this? I registered the domains to protect my business name, but now I seem to have caused another problem by doing so.