What else are you feeding them? I would seperate them for a little bit, to see who’s poop/urine smells so bad (I would probably think the younger one)

I’m going to take a guess and say that your little girl is actually a little boy. At 3 months and with the onion smell, it’s very likely that your bun is becoming sexually mature. Some male rabbits are known for their onion-y smelling markings. Male and female genitalia in rabbits are also very similar!

This is a good article on sexing rabbits. WARNING: Does include large pictures of rabbit genitals. That’s probably obvious, but I thought I should add in a warning. http://www.rabbitnetwork.org/articles/sexing.shtml

I also suggest you look into some of links about what veggies to feed your rabbits. Carrots are very high in sugar and should only be fed in small amounts as an occasional treat. Basil is a good herb to feed, but one leaf every other day is not enough veggies. They should be be getting a minimum of 2 cups of veggies (predominately leafy greens) for every 6 ibs. You’d want to introduce the new veg slowly though.

http://rabbit.org/faq-diet/
http://rabbit.org/suggested-vegetables-and-fruits-for-a-rabbit-diet/
https://binkybunny.com/BUNNYINFO/VeggieList/tabid/144/Default.aspx

I have a young male rabbit approaching sexual maturity and since the first time he started pooping, I thought it smelled like onions.  

With the males, it’s the urine (when they mark) that smells like onions. But since they usually poop and pee in the same area it makes it all smell onion-y. I remember when Ox was unneutered he’d make the entire room smell like onion even though he was only marking his litter box! Bleh!

I have had 2 female (spayed) rabbits, who sometimes had poop that smelled like onions.

Buns of either sex can spray and mark, the oily stuff smells onion-y. I think it’s more often associated with boys, but girls can smell too.

I’ve never heard of girls smelling onion-y before. I learn new things every day on here!