Oh man, that's why i didn't bought the Fated Engram and instead, logged in with a different character to discover that he was selling Riskrunner - they are looking into the issue now.

It sounds like, based on other reports, that Xur's inventory was bugged. You tried to purchase it directly from Xur unsuccessfully. You then purchased a fated engram, which actually dropped the Cerberus auto-rifle. By the time you got back to Xur, his inventory had updated (to where he was selling Riskrunner) and that your fated engram was not reset because you'd already gotten Cerberus from the one you purchased. Again, based on other reports, i don't know that anyone was actually able to purchase the Cerberus directly from Xur. Every report i've read said they that saw Cerberus in his inventory but were unable to purchase it. Upon going to orbit and returning to EDZ, Cerberus had been replaced by Riskrunner, which people have been able to purchase as normal. It sounds like Bungie accidentally had Cerberus in Xur's inventory, but disabled the ability to purchase it long enough to get the inventory updated. While it might've cost you more in shards, you got the gun you wanted, it just came from the fated engram and not directly from Xur's inventory.