I would be getting your DD checked for a Urinary Tract Infection, just to be on the safe side. We had the same smelly wee situation (I also thought he had done poos) with our DS when he was only 10 weeks old, I got fobbed off by 3 doctors when I asked about it being a UTI, they said he was too young to get one, especially as he was a boy. It ended up that he did have a UTI. I'm not saying that your DD has one, but, I would definently get smelly wee checked out and do not let the doctors fob you off, demand a urine test.
I don't know if this would have any relation to your breast/bottle problem, but the hospital (where he eventually ended up) was asking me if he was fussy or not eating.
ETA: I didn't mean to panic you about this, but, it is such an easy/painless test to do you might as well get her checked out just to be safe. She probably is too young to get a UTI, but it's always good to be sure, as there are always exceptions. (like my DS)