To answer the question, your edges were manifold, your vertices were not. Your edges were connected to other edges, making them complete. The vertices, on the other hand, did not connect to something it thought it should have, creating a void.
If no possible camera angle can see the bad edge, you should be ok with animation/video games(like on a foot inside a shoe), but 3d printing needs manifold.
So, whats wrong with the vertices? They are allowing the camera to see inside a dimension it doesnt like. Like, if you were the architect of the world, you wouldnt want video-game-style clipping in the alps, so you would ensure that general area be rendered manifold