Can two individuals be biologically incompatible?

The reason i ask is because my girlfriend had a bad physical reaction after having with her former boyfriend. They had to break up because it was too dangerous for her health. Now, even though we have not had , the same thing seems to be happening with us. There has been some fooling around though. Infections seem to be extremely sudden and provoked by the slightest form of contact. Any suggestions, any doctors out there that could point me in the right direction in terms of research. Thank you all.