Hi there. This is actually how Exotic Ciphers have worked since they were added to Xur. Players must have an open space in their inventory to receive one or else they are lost [url=https://help.bungie.net/hc/en-us/articles/360048717732-Deleted-Item-and-Character-Policy]and cannot be returned[/url].
Unfortunately you'll have to wait until next week to do the quest again or see if you have a Cipher from this season's past or last season you can still claim.
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Yes, but it's poor development to not suspect this and give no warning to players for system years in place. Luckily Bungie devs listen to improvement requests. Considering most don't have a full inventory, not many fall victim to this. Hopefully, the Bungie dev will add a warning to the cipher quest. I think it would be fair for a dev to give everyone one freebee if they're is no warning, and this is their first time. After all, getting god rolls for Hawkmoon and DMT are rare and expensive.