Question about urine sample at doctors office

jo

I went to the ER on Sunday- it’s Wednesday morning now- and was told I had a UTI. They put me on meds, so today will be day three of taking them.

Anyway, I woke up this morning with really awful back pain on my left side again, which the dr at the ER said was due to the UTI. I had my routine prenatal appt yesterday, and they tested my urine like always, but never said anything about it. Would their routine test have found anything? (kidney infection, lingering UTI, kidney stone)?

Also, what could this pain still be coming from??