If I understand the upgrade finder instructions properly, you run a BiB first so that it knows what gear you already have. It then should not list gear you already have as upgrades you want to go hunting for.
However, it lists several legendary items that I already own as upgrades to my current gear (which I suppose they are to the items that I have equipped).
I can't confirm for sure, but I think many, if not all, of these are legendaries that I looted as 940 and have since upgraded to 970, but honestly I'm not 100% sure of this. I do keep legendaries that I am not currently using in the bank, but I have made sure, several times, to open bank before clicking the AMR addon doohickey. (I also just tried it again after moving all legendaries into bag inventory, but the behavior did not change)
How can I get it to ignore the legendary items I've already got? (I'm using the list to target which relinquished tokens I buy with Veiled Argunite, and it's a little tedious looking at the upgrade list, thinking, "I'm pretty sure I have those shoulders already" and having to go back to Dalaran to double-check my bank before buying the tokens.