Yes it could be in your bowels. I had problems like this before w/ endo and when I got the endometrioma removed and some clean up, I didn't have problems for years. I didn't have endo actually in the bowels that time (just some adhesions bothring things). Getting pregnant 2x in there really helped (since b/t the hormone changes and immune suppression of pregnancy controls/kills off the endo).
Just recently when I had surgery for endo, I was found to have actual endo implants everywhere. It's so gross, but it is in my rectum (from inside out)and bowels. The only good news is that I'm done having children and not too many years out from menopause anyway, so getting my ovaries removed was an option for me and I hope that this will get the endo in those places under control. It's so disgusting how it goes everywhere. When I saw all the pictures this time, I felt like vomitting.
Yes, if you have those problems then it is possible that you have endometriosis affecting your intestinal system. Over time, some scar tissue (aka adhesions) can form. For the most part, usually women just muddle through until they reach menopause and then the problem goes away.