It sounds very possible that your baby may have stones/crystals, and even though they did an x-ray, x-rays don't show all types of stones. There are stones/crystals that only show on an ultraound. My yorkie gets ammonium urate stones which are not visible on x-rays, only on ultrasounds.
Honestly, I would have an u/s done to determine if she has them...
Also, the vet should be able to get a sample himself. Actually, I prefer that the vet usually take the sample so that it's not contaminated in any way. Definitely have them do a urine culture along with the urinalysis.
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