My sim moved in with the Charm household, as the story went she was the long lost granddaughter of Minerva Charm.
Anyway, after several game hours, I noticed Minerva really had to pee, but wasn't doing anything about it. I discovered she had no option to Use when I clicked a toilet! Clicking the bar to auto resolve, she would do the "I can't do that" thought bubble and shrug. Fortunately I have MCCC, and going through her hidden traits, she was missing "Toilet Use Sitting." Once I gave her that, she was fine.
No matter how hastily I throw a sim together, or what weird combo of custom gender options I choose, I've never had a sim who didn't know how to use a toilet before!
