Looks like a vertex normal problem. Did you tweak the vertex normals? You may have more than one vertex normal for every vertex.
A quick fix would be to export it as an obj and re-import it.
Make a hotkey for the toggle normal display and make it a habit to check your normals every now and then, especially before you combine and merge vertices. Also, the more you get a grip on how the poly tools work the more you will know what to expect and anticipate possible situations when normal normals would be reversed cause you used a certain tool.