Chances of you being 12 weeks pregnant and still getting a negative pregnancy test is very slim. You may have several things goin on here. Vegetarians often don't get enough folate and iron in their diets and thus become anemic which can make you feel very sick. This happened to my friend. You may also have a cyst on an ovary or something.
Cysts are very common and usually benign.
Also, there is NO WAY your doctor could know if you have endometriosis just by looking at you. The only way a doctor can know if you have it for sure is to go in surgically and look around and actually see it. It is under the influence of the hormones so it grows and sheds just like your period and when it sheds in the abdomen it can really painful as the body tries to reabsorb it. 1st of all, my period is like clockwork, and last 4 to 5 days tops. I've never missed a period in my life.