Alphinaud and his sister periodically swap places, no one ever even realizing.
Papalymo once attempted an experimental spell that permanently damaged Yda's mind, and thus he remains around her all the time out of guilt.
Thancred once attempted to court Minfilia, but she was so oblivious he gave up after three pickup lines.
Lolorito is actually two members on the Syndicate. He personally hires the Aesthetician to change his facial hair back and forth when he removes his mask and puts it back on.
The Coco brothers (Thaumaturge Guild Leaders) are actually one person split in six by a magical accident. This is why Cocobusi doesn't have a lot of aether; there wasn't enough left over fror him after the other five split.
Rhauban has a rabid sweet tooth, and avoids eating anything sweet lest he binge on sugar.
Nanamo has drunk three Roegadyn under the table in the past and not even shown the slightest sign of tipsiness.
Kan-E-Senna sometimes talks to herself to aid her thinking process, and when others see her at it, passes it off as talking to the Elements.
Merlwyb secretly suffers from Seasickness when in deep waters.
Cid has a secret obsession, to create an artificial lifeform with Magitech, the first Artificial Intelligence.