I have this problem quite a bit and I can not figure out why. I have looked up many posts in several forums but no one seems to have had this problem (that I can find). This appears to be a bug in the intersecting faces part of the 3d printing plugin. It happens in both 2.8 and 2.79b.
In this model I have 2 intersecting faces, yet they are not as you can see. Other times I have faces intersecting at a vertex, but again are not intersecting as they are just sharing that vertex. If I triangulate this model, it will have several intersecting faces at shared vertices, some of which do not exist now. I have also had models where I change something and the intersecting faces will disappear, even when I haven't touched them.