Are there any diseases that can be misdiagnosed as endometriosis or vice versa?

Yes: Actually one very common misdiagnosis is interstitial cystitis which is an inflammatory condition of the bladder that frequently causes pelvic pain and painful sex.

There are several: But interstitial cystitis and irritable bowel syndrome are two culprits of abdominopelvic pain that are always in the differential. Certain elements of your history can help differentiate them from eachother and your doctor is best at guiding you there. Painful periods are a common presenting symptom of endometriosis but other causes (fibroids being a possibility) can exist 2 & warrant eval by gyn.