So, most advantages can't be doubled up. Only 4 can that I see: Sorcery, Duelist, Reputation, and Quick Reflexes.
I'm having a problem with a corner case in backgrounds though. Typically, if you get an advantage from backgrounds twice, you cross one off and take another of the same value. Sorcery is called out as an exception to this. Duelist and Reputation only show up on one background each, so they're not a problem. But a Mousquetaire Explorer is a problem, as they both give Quick Reflexes.