False positive chlamydia result?

I'm 30 yo. Before the start and the end of each relationship I make sure that I get tested for all STD/STIs and that I am clean. I got into a new relationship 2 months ago. My new partner told me he got tested for both blood and urine and was clean. I started having weird discharge and felt itchy down there. Went to my doctor. Got treated for yeast infection. Left samples for urine just in case. I got result back yesterday and tested positive for chlamydia. I took medicine immediately and needless to say, had a serious talk with my partner. He looked genuinely surprised and took the mediation I bought for him immediately. Made an appointment with his doctor for tmr. From his reaction I don't think he was lying to me...but it's too late to get re-tested at this point since we both took the medication already... I'm feeling confused and frustrated about the whole situation. I guess I'm just looking for some support here...