Transparency up-front: I have not read through 17 pages to see if these have already been posted. This for PC.
Problem 1: After completing the "Heroes" mission, there are two copies of La Chingona Dorada which spawn at Coyote Cojo. This is consistent with the game behavior pre-1.6. There used to be an issue of a third copy randomly dropping on the street somewhere, but this is not that. After picking up two pistols, two pistols appear in inventory. So far so good. One pistol may be upgraded and the other ... ??? Absolutely no idea. It's not available for upgrade, it's in inventory, but not available to equip or upgrade... it's just (beats me). Kinda freaky to pick up two things, see two things in inventory, and then find out there's really only one thing and the other just kind of poofed somewhere along the line.
Problem 2: Concurrently with that, upgrading iconics is just kind of funky post-1.6. If you upgrade from Rare to Epic to Legendary, then you end up with a Rare, an Epic and a Legendary showing on the inventory screen. The Rare and Epic versions are not available to upgrade, nor can they be equipped, but they do show on the inventory screen. Exiting the game and restarting seems to clear out the extra copies, so it's not like it's they're persistent. Here's three copies each of Widow Maker and Fenrir (Rare, Epic, and Legendary), but only the Legendary is real:
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