That's what I'm saying and I'm not considering this a bug.
This is something for the feedback section: http://forums.thesims.com/en_US/categories/the-sims-4-feedback
What the OP is saying (I believe) is that they attempted to make a transgender woman by choosing a masculine body frame with a feminine name and clothing. But the game equates masculine body frame to male pronouns (he/him) and family relations (father/son). It's not a bug exactly, but it's definitely not optimal as it's misgendering to force a person with a masculine body frame to use male pronouns if they don't want to.
The workaround I'd suggest for creating a trans woman would be to use the feminine body frame and set the options to use the toilet standing up and make others pregnant rather than getting pregnant (or turn off the ability to get or make others pregnant for that Sim altogether). It's still not perfect, but that is what I would do (I'm a non-binary trans person myself for the record).
@giddygeekgrin Could you clarify what gender your Sim had ?
