Bungie is aware of the issue, and they are working on a change: [quote]- Players who complete the Xenology quest from Xur while already having an Exotic Cipher in their inventory will have the quest removed with no reward. [/quote] For now, you just have to make sure that you have space in your inventory before collecting a cipher. Source: https://www.bungie.net/en/Explore/Detail/News/50129