I took some for the same reason. The only side effects I had was upset stomach and cramps. But that's just me.. Everyone has different side effects.
Personally I'd take them or your infection can get worse and turn into a kidney infection. If your doctor had a concern with antibiotics while pregnant they wouldn't have prescribed it for you! You can always call your doctor and ask them about your concerns
I've taken antibiotics 3 times throughout my pregnancy for UTI's. I'm only 19 weeks. You should be fine.
Your doctor wouldn't give you antibiotics if it wasn't ok.