Xander is right. I think you might find that the "Keep Faces Together" option was unticked.

You would see it as the two faces extruding together, but in reality once you do a smooth or proxy smooth you would see that they are two separate pieces of geometry.

If u are 100% sure "Keep Faces Together" was ticked then you may need to look at the history for the extrusions and see what the settings are, as it may give you a clue to what went wrong.