I don’t understand clearly what’s going on here. I selected all the faces before extruding but it looks like something was left behind?
A common issue here is that the curve creates several vertices at the center point. When that happens the odds of faces beneath the faces on top are pretty good. Removing doubles won’t work on them because they are spaced out properly from one another that if the merge distance was increased there would be damage to the model. The only way to solve it is to delete those faces then select the previous edge loop, extrude (E) and size (S) to 0.