Factual error: The poem Isolde recites, John Donne's "The Good-Morrow", is a 17th-century work, which is centuries later than the movie's time period.
Factual error: In the scene where Tristan is making his return from Ireland and the crowd is gathering around him there are two hens in the foreground. One is a Rhode Island Red and the other is a Black Plymouth Rock. Both of these are American breeds of chicken and did not appear until many hundreds of years after this film is set.
Answer: Without going into detail, two possible birth control options would be the withdrawal method or earlier versions of condoms. It's unlikely that Marke and Isolde were using these methods, because Marke, as a king, would probably want children to be his heirs. But Isolde might have at least been taking precautions with Tristan, especially during the time that she was betrothed to Morholt. There would be trouble if she became pregnant while her betrothed was away. Also, as Tailkinker wrote, maybe she simply did not conceive.