The boons my party is finding don't seem to be subject to vault limits. So far, in scenario B-1, I found and acquired 4 Codexes, and in B-1 I found Father Zantus, and then in B-2 I found a second Father Zantus. I haven't swapped any characters in or out of the party.

 

1.1.6.1, iPad Air, iOS 8.4.

Bumping to provide my own test cases for this:

 

https://forums.obsidian.net/topic/90753-already-acquired-cards-appearing-in-scenarios/

Bump. This is still a problem.

I've run into this too, except with the deathbane crossbow so I didn't really mind. I think this also affected banes, since I ran into 2 Enchanters in a row.

Yes, I just found two Enchanters in the same deck, too.