Looking for endometriosis during surgery is a little bit like searching for Waldo in a cartoon crowd. Except instead of painstakingly scanning the images of an agoraphobe's worst nightmare for that red and white striped turtleneck, imagine yourself the surgeon--meticulously dissecting an entirely different type of circus or zoo for an entirely different red-white colored culprit.
Endometriosis is the Waldo of the uterus for a number of reasons. For starters, endometriosis comes with a spectrum of symptoms. One woman might complain of horrible menstrual cramps and pain with defecation during her period, and another might not report much pain at all. Studies have also shown that the severity of pain a woman experiences has little correlation with actual surgical findings in endometriosis, so it probably doesn't make much sense to go surgically hunting for endometriosis in the first place.
Endometriosis is also elusive. It's not always in the tubes or on the ovaries, just like Waldo is not always on the merry-go-round or in the lion's cage. If this analogy holds up however, you'll soon understand why doctors sometimes go searching for it in seemingly ridiculous places, like the lungs.
Why in the world would endometriosis turn up in your lungs? For the same reason that Martin Handford would hide Waldo in a lion's cage, I guess--because it/he can. And the lungs aren't the only crazy place doctors have reported finding endometriosis. They've found it in the arm, thigh, diaphragm, pleura, trachea, vagina, and surgical scars, like those from Cesarean sections.
The reason why these abnormal pieces of uterine lining end up in odd, even dangerous places is still a mystery. And it's worth pointing out that most often, endometriosis will "stay put." (Staying put for endometriosis meaning in the tubes, on the ovaries, and surrounding the uterus on the peritoneal and recto-vaginal pouch lining.)
Some of the theories of uterine tissue travel include: retrograde menstruation (or trans-tubal travel) where the lining migrates backwards into the tubes and towards the ovaries instead of going out the vagina as a period; an immune system problem that contributes to extra-uterine deposits; spread through the blood and/or lymphatics systems; genetic predisposition; and surgical transplantation.
The last theory might explain the rare occurrence where pockets of endometrial tissue are found in scars from C-sections, episiotomies, and appendectomies even. Surgical scar endometriomas, as they are called, are thought to occur when abnormal uterine tissue comes into direct contact with and implants onto normal healing tissue. According to several case report studies, they are extremely rare and easily remedied by surgically removing the transplanted pocket of tissue.
In medicine, there's a saying, "Don't go zebra hunting," which means if something is wrong, the answer is most likely a common diagnosis and not some crazy or rare disease. The same is true for endometriosis. If you have it, it's most likely going to be in the common places like the tubes and ovaries, despite what years of candy-cane striped sleuthing have taught you.
SOURCES:
http://www.mayoclinic.com/health/endometriosis/DS00289/DSECTION=causes
http://www.ivf.com/endoassn.html
Lee CH, et all. Thoracic Endometriomas: rare presentation as a solitary pulmonary nodule with eccentric cavitations. Thorax 2009;64:919-920 doi:10.1136/thx.2008.111294
Watanabe M, et al. Surgical Scar Endometrioma. Surg Gynecol Obstet. 1993 Sep;177(3):243-6.