Been happening for a while. Having "Prioritize Equipped Gems" chosen, it will choose gems that cap at 50 and try and upgrade them, stopping you from completing the rift. Even if they are greyed out at the bottom of the Adventuror config
I assumed it was Adventurer that handles the upgrading of Legendary Gems, but it appears it is actually QuestTools. With that being said, QuestTools does not seem to have any checks in the upgrade process if the gem is max rank or not.
To fix this, first contact the current developer and inform them, secondly you can go into your "Demonbuddy\Plugins\QuestTools\ProfileTags" folder, and inside the CompleteGreaterRiftTag.cs file, paste this line of code on Line 249: