My cat was spayed at 2 pounds. Can that mess up her urinary tract?

It isn't the spay, it's probably because the UTI hasn't gone away. That dark and smelly urine is a give away. Take her back to the vet, or call - it's time for a different antibiotic. It very often takes more than one round of antibiotic, or a stronger one, to kill the bacteria. In the meantime, if you're feeding her dry food, stop. Switch to an all canned diet to keep her better hydrated. Dry foods are a big contributor to UTI's as cats don't drink much, and the dry food dehydrates them. The urine stays in the bladder longer, and that gives bacteria a chance to build up and UTI's to form.

Sounds as if she does have a urniary infection. When she pees it's painful and she associates the litter box with that pain. So that is why she goes elsewhere. You need to take her to your Vet and he will probably prescribe Baytril or Amoxi-Drops for 7 days. (twice a day) He might also give you a powder or gel to put into her food to help elivate the acid/PH in her urnine (that's the cause of the strong smell).

But having her spayed when she was only 2 pounds had nothing to do with the infection. Also, if her urine is dark, she is probably passing alittle blood. You need to get her to your Vet ASAP and following his directions. She is extremely uncomfortable and in pain now.

Good Luck

YES IT WILL BECAUSE SPAYING IS CRUEL!!!!!!!!!!!!!!!!!!!!!!! YOU SHOULD NEVER HAVE DONE THAT IN THE FIRST PLACE AND YOU SHOULD NEVER DO IT TO ANY OTHER PETS!