Recently I had an advanced Urinary tract infection which turned out to be a kidney infection. I hate having a UTI. They suck. It hurts to pee! And I was drink Alot of cranberry juice. 2 gallons in 1 week. all I drank was cranberry and plum juice. The plum juice was not a good Idea it made my tummy very gurgly. And I am still on my antbiotics. They gave the good stuff. Here's a hint for getting rid of the pain during a UTI: take AZO, but you have to wait 24 hours before you take a urine test. It'll turn your pee orange, don't worry it's harmless.
The antibiotics were probably as responsible for your stomach upset as anything. If it continues, you can try a probiotics like yogurt or kefir to help return everything back to normal.