Press ctrl N to recalc normals. However, I may be wrong but it sounds like you have faces inside the model? If you do, recalculating normals does nothing. Whenever you extrude, it always deletes the original face if you won't be able to see it anyway, which usually means its inside the model. Heres a quick example:
Here is a basic shape:
I extrude the middle:
If you look, the orginal face is gone, because it is no longer needed:
If I remake the original face like this:
It causes problems visually:
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