Even in 2.7x this can happen if you arrange modifiers in certain ways. And even if there is only one face dot, it can appear offset.
This is 2.79 with modifiers:
Currently at least, face dots also often half penetrate the surface mesh.
The main issue though, is that it adds extra clutter in various ways that makes it harder to read mesh topology, especially with dense meshes.
Zero-sized faces and differetiating between edge and face select modes can be handled in ways that doesn’t require littering face select mode with noisy dots that makes it hard to see your mesh.
- For zero-sized faces, we could have a dot show only for those, or some other visual marker.
- For differentiating between edge and face select modes, we could make edges less prominent in face select mode, for example.