There was a bug where players would get the extra loot (including Bonus Chance for the Ascension Item, Emblems and Atlantis Coins) when joining the Alliance after Rare Titan spawned. This was not intended behavior, as defined in the 1.12 release notes:
The bonus chance is only available for players who are already part of the alliance when the Rare Titan appears)
Unfortunately, there seems to have been an issue with this fix we implemented yesterday which resulted in inconsistencies in received Titan Loot for those who joined the Alliance after the Titan spawned. We believe we have now fixed this issue. Receiving Titan Bonus Loot should now only be possible for those who were present when Rare Titan spawned. Our apologies for any inconvenience caused by this!