I’m doing BlenderGuru’s anvil tutorial to re-learn Blender after not using it for almost two years. After doing boolean modifier to remove part of the original mesh, he corrects some ngons to be quads, which I also do. After he does it, in face mode a vertex he previous has showing disappears, whereas mine will not go away. The only thing I do differently (because I’m in 2.79 and he’s using a 2.78 version) is when doing the boolean modifier I have to change the modifier variable BMesh to Carve, otherwise it doesn’t interact with the mesh I’m trying to adjust. I’m pretty much at a loss at this point.
Mine and his after correcting ngons (all faces definitely have 4 vertices now):
Mine right after correcting ngons applying subsurface modifier (takes into account the phantom vertex):
His after applying subsurf modifier: